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38 * \brief Implements functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels
40 * \author Berk Hess <hess@kth.se>
41 * \ingroup module_nbnxm
46 #include "pairlist_tuning.h"
55 #include "gromacs/domdec/domdec.h"
56 #include "gromacs/hardware/cpuinfo.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdlib/calc_verletbuf.h"
59 #include "gromacs/mdtypes/commrec.h"
60 #include "gromacs/mdtypes/inputrec.h"
61 #include "gromacs/mdtypes/interaction_const.h"
62 #include "gromacs/mdtypes/state.h"
63 #include "gromacs/pbcutil/pbc.h"
64 #include "gromacs/topology/topology.h"
65 #include "gromacs/utility/cstringutil.h"
66 #include "gromacs/utility/fatalerror.h"
67 #include "gromacs/utility/gmxassert.h"
68 #include "gromacs/utility/logger.h"
69 #include "gromacs/utility/strconvert.h"
70 #include "gromacs/utility/stringutil.h"
72 #include "nbnxm_geometry.h"
73 #include "pairlistsets.h"
75 /*! \brief Returns if we can (heuristically) change nstlist and rlist
77 * \param [in] ir The input parameter record
79 static bool supportsDynamicPairlistGenerationInterval(const t_inputrec &ir)
82 ir.cutoff_scheme == ecutsVERLET &&
84 !(EI_MD(ir.eI) && ir.etc == etcNO) &&
88 /*! \brief Cost of non-bonded kernels
90 * We determine the extra cost of the non-bonded kernels compared to
91 * a reference nstlist value of 10 (which is the default in grompp).
93 static const int nbnxnReferenceNstlist = 10;
94 //! The values to try when switching
95 const int nstlist_try[] = { 20, 25, 40, 50, 80, 100 };
96 //! Number of elements in the neighborsearch list trials.
97 #define NNSTL (sizeof(nstlist_try)/sizeof(nstlist_try[0]))
98 /* Increase nstlist until the size of the pair-list increased by
99 * \p c_nbnxnListSizeFactor??? or more, but never more than
100 * \p c_nbnxnListSizeFactor??? + \p c_nbnxnListSizeFactorMargin.
101 * Since we have dynamic pair list pruning, the force kernel cost depends
102 * only very weakly on nstlist. It depends strongly on nstlistPrune.
103 * Increasing nstlist mainly affects the cost of the pair search (down due
104 * to lower frequency, up due to larger list) and the list pruning kernel.
105 * We increase nstlist conservatively with regard to kernel performance.
106 * In serial the search cost is not high and thus we don't gain much by
107 * increasing nstlist a lot. In parallel the MPI and CPU-GPU communication
108 * volume as well as the communication buffer preparation and reduction time
109 * increase quickly with rlist and thus nslist. Therefore we should avoid
110 * large nstlist, even if that also reduces the domain decomposition cost.
111 * With GPUs we perform the dynamic pruning in a rolling fashion and this
112 * overlaps with the update on the CPU, which allows even larger nstlist.
114 // CPU: pair-search is a factor ~1.5 slower than the non-bonded kernel.
115 //! Target pair-list size increase ratio for CPU
116 static const float c_nbnxnListSizeFactorCpu = 1.25;
117 // Intel KNL: pair-search is a factor ~2-3 slower than the non-bonded kernel.
118 //! Target pair-list size increase ratio for Intel KNL
119 static const float c_nbnxnListSizeFactorIntelXeonPhi = 1.4;
120 // GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel.
121 //! Target pair-list size increase ratio for GPU
122 static const float c_nbnxnListSizeFactorGPU = 1.4;
123 //! Never increase the size of the pair-list more than the factor above plus this margin
124 static const float c_nbnxnListSizeFactorMargin = 0.1;
126 void increaseNstlist(FILE *fp, t_commrec *cr,
127 t_inputrec *ir, int nstlist_cmdline,
128 const gmx_mtop_t *mtop,
130 bool useOrEmulateGpuForNonbondeds,
131 const gmx::CpuInfo &cpuinfo)
133 if (!EI_DYNAMICS(ir->eI))
135 /* Can only increase nstlist with dynamics */
139 float listfac_ok, listfac_max;
140 int nstlist_orig, nstlist_prev;
141 real rlist_inc, rlist_ok, rlist_max;
142 real rlist_new, rlist_prev;
143 size_t nstlist_ind = 0;
144 gmx_bool bBox, bDD, bCont;
145 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";
146 const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
147 const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
148 const char *box_err = "Can not increase nstlist because the box is too small";
149 const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
152 if (nstlist_cmdline <= 0)
154 if (ir->nstlist == 1)
156 /* The user probably set nstlist=1 for a reason,
157 * don't mess with the settings.
162 /* With a GPU and fixed nstlist suggest tuning nstlist */
164 useOrEmulateGpuForNonbondeds &&
165 ir->nstlist < nstlist_try[0] &&
166 !supportsDynamicPairlistGenerationInterval(*ir))
168 fprintf(fp, nstl_gpu, ir->nstlist);
172 while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
176 if (nstlist_ind == NNSTL)
178 /* There are no larger nstlist value to try */
183 if (EI_MD(ir->eI) && ir->etc == etcNO)
187 fprintf(stderr, "%s\n", nve_err);
191 fprintf(fp, "%s\n", nve_err);
197 if (ir->verletbuf_tol == 0 && useOrEmulateGpuForNonbondeds)
199 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");
202 if (ir->verletbuf_tol < 0)
206 fprintf(stderr, "%s\n", vbd_err);
210 fprintf(fp, "%s\n", vbd_err);
216 GMX_RELEASE_ASSERT(supportsDynamicPairlistGenerationInterval(*ir), "In all cases that do not support dynamic nstlist, we should have returned with an appropriate message above");
218 if (useOrEmulateGpuForNonbondeds)
220 listfac_ok = c_nbnxnListSizeFactorGPU;
222 else if (cpuinfo.brandString().find("Xeon Phi") != std::string::npos)
224 listfac_ok = c_nbnxnListSizeFactorIntelXeonPhi;
228 listfac_ok = c_nbnxnListSizeFactorCpu;
230 listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
232 nstlist_orig = ir->nstlist;
233 if (nstlist_cmdline > 0)
237 sprintf(buf, "Getting nstlist=%d from command line option",
240 ir->nstlist = nstlist_cmdline;
243 ListSetupType listType = (useOrEmulateGpuForNonbondeds ? ListSetupType::Gpu : ListSetupType::CpuSimdWhenSupported);
244 VerletbufListSetup listSetup = verletbufGetSafeListSetup(listType);
246 /* Allow rlist to make the list a given factor larger than the list
247 * would be with the reference value for nstlist (10).
249 nstlist_prev = ir->nstlist;
250 ir->nstlist = nbnxnReferenceNstlist;
251 const real rlistWithReferenceNstlist =
252 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
254 ir->nstlist = nstlist_prev;
256 /* Determine the pair list size increase due to zero interactions */
257 rlist_inc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j,
258 mtop->natoms/det(box));
259 rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_ok) - rlist_inc;
260 rlist_max = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_max) - rlist_inc;
263 fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
264 rlist_inc, rlist_ok, rlist_max);
267 nstlist_prev = nstlist_orig;
268 rlist_prev = ir->rlist;
271 if (nstlist_cmdline <= 0)
273 ir->nstlist = nstlist_try[nstlist_ind];
276 /* Set the pair-list buffer size in ir */
278 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, -1, listSetup);
280 /* Does rlist fit in the box? */
281 bBox = (gmx::square(rlist_new) < max_cutoff2(ir->ePBC, box));
283 if (bBox && DOMAINDECOMP(cr))
285 /* Check if rlist fits in the domain decomposition */
286 if (inputrec2nboundeddim(ir) < DIM)
288 gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
290 bDD = change_dd_cutoff(cr, box, gmx::ArrayRef<const gmx::RVec>(), rlist_new);
295 fprintf(debug, "nstlist %d rlist %.3f bBox %s bDD %s\n",
296 ir->nstlist, rlist_new, gmx::boolToString(bBox), gmx::boolToString(bDD));
301 if (nstlist_cmdline <= 0)
303 if (bBox && bDD && rlist_new <= rlist_max)
305 /* Increase nstlist */
306 nstlist_prev = ir->nstlist;
307 rlist_prev = rlist_new;
308 bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
312 /* Stick with the previous nstlist */
313 ir->nstlist = nstlist_prev;
314 rlist_new = rlist_prev;
326 gmx_warning("%s", !bBox ? box_err : dd_err);
329 fprintf(fp, "\n%s\n", !bBox ? box_err : dd_err);
331 ir->nstlist = nstlist_orig;
333 else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
335 sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
336 nstlist_orig, ir->nstlist,
337 ir->rlist, rlist_new);
340 fprintf(stderr, "%s\n\n", buf);
344 fprintf(fp, "%s\n\n", buf);
346 ir->rlist = rlist_new;
350 /*! \brief The interval in steps at which we perform dynamic, rolling pruning on a GPU.
352 * Ideally we should auto-tune this value.
353 * Not considering overheads, 1 would be the ideal value. But 2 seems
354 * a reasonable compromise that reduces GPU kernel launch overheads and
355 * also avoids inefficiency on large GPUs when pruning small lists.
356 * Because with domain decomposition we alternate local/non-local pruning
357 * at even/odd steps, which gives a period of 2, this value currenly needs
358 * to be 2, which is indirectly asserted when the GPU pruning is dispatched
359 * during the force evaluation.
361 static const int c_nbnxnGpuRollingListPruningInterval = 2;
363 /*! \brief The minimum nstlist for dynamic pair list pruning.
365 * In most cases going lower than 4 will lead to a too high pruning cost.
366 * This value should be a multiple of \p c_nbnxnGpuRollingListPruningInterval
368 static const int c_nbnxnDynamicListPruningMinLifetime = 4;
370 /*! \brief Set the dynamic pairlist pruning parameters in \p ic
372 * \param[in] ir The input parameter record
373 * \param[in] mtop The global topology
374 * \param[in] box The unit cell
375 * \param[in] useGpuList Tells if we are using a GPU type pairlist
376 * \param[in] listSetup The nbnxn pair list setup
377 * \param[in] userSetNstlistPrune The user set ic->nstlistPrune (using an env.var.)
378 * \param[in] ic The nonbonded interactions constants
379 * \param[in,out] listParams The list setup parameters
382 setDynamicPairlistPruningParameters(const t_inputrec *ir,
383 const gmx_mtop_t *mtop,
385 const bool useGpuList,
386 const VerletbufListSetup &listSetup,
387 const bool userSetNstlistPrune,
388 const interaction_const_t *ic,
389 PairlistParams *listParams)
391 listParams->lifetime = ir->nstlist - 1;
393 /* When nstlistPrune was set by the user, we need to execute one loop
394 * iteration to determine rlistInner.
395 * Otherwise we compute rlistInner and increase nstlist as long as
396 * we have a pairlist buffer of length 0 (i.e. rlistInner == cutoff).
398 const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
399 int tunedNstlistPrune = listParams->nstlistPrune;
402 /* Dynamic pruning on the GPU is performed on the list for
403 * the next step on the coordinates of the current step,
404 * so the list lifetime is nstlistPrune (not the usual nstlist-1).
406 int listLifetime = tunedNstlistPrune - (useGpuList ? 0 : 1);
407 listParams->nstlistPrune = tunedNstlistPrune;
408 listParams->rlistInner =
409 calcVerletBufferSize(*mtop, det(box), *ir,
410 tunedNstlistPrune, listLifetime,
413 /* On the GPU we apply the dynamic pruning in a rolling fashion
414 * every c_nbnxnGpuRollingListPruningInterval steps,
415 * so keep nstlistPrune a multiple of the interval.
417 tunedNstlistPrune += useGpuList ? c_nbnxnGpuRollingListPruningInterval : 1;
419 while (!userSetNstlistPrune &&
420 tunedNstlistPrune < ir->nstlist &&
421 listParams->rlistInner == interactionCutoff);
423 if (userSetNstlistPrune)
425 listParams->useDynamicPruning = true;
429 /* Determine the pair list size increase due to zero interactions */
430 real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j,
431 mtop->natoms/det(box));
433 /* Dynamic pruning is only useful when the inner list is smaller than
434 * the outer. The factor 0.99 ensures at least 3% list size reduction.
436 * With dynamic pruning on the CPU we prune after updating,
437 * so nstlistPrune=nstlist-1 would add useless extra work.
438 * With the GPU there will probably be more overhead than gain
439 * with nstlistPrune=nstlist-1, so we disable dynamic pruning.
440 * Note that in such cases the first sub-condition is likely also false.
442 listParams->useDynamicPruning =
443 (listParams->rlistInner + rlistInc < 0.99*(listParams->rlistOuter + rlistInc) &&
444 listParams->nstlistPrune < listParams->lifetime);
447 if (!listParams->useDynamicPruning)
449 /* These parameters should not be used, but set them to useful values */
450 listParams->nstlistPrune = -1;
451 listParams->rlistInner = listParams->rlistOuter;
455 /*! \brief Returns a string describing the setup of a single pair-list
457 * \param[in] listName Short name of the list, can be ""
458 * \param[in] nstList The list update interval in steps
459 * \param[in] nstListForSpacing Update interval for setting the number characters for printing \p nstList
460 * \param[in] rList List cut-off radius
461 * \param[in] interactionCutoff The interaction cut-off, use for printing the list buffer size
463 static std::string formatListSetup(const std::string &listName,
465 int nstListForSpacing,
467 real interactionCutoff)
469 std::string listSetup = " ";
470 if (!listName.empty())
472 listSetup += listName + " list: ";
474 listSetup += "updated every ";
475 // Make the shortest int format string that fits nstListForSpacing
476 std::string nstListFormat = "%" + gmx::formatString("%zu", gmx::formatString("%d", nstListForSpacing).size()) + "d";
477 listSetup += gmx::formatString(nstListFormat.c_str(), nstList);
478 listSetup += gmx::formatString(" steps, buffer %.3f nm, rlist %.3f nm\n",
479 rList - interactionCutoff, rList);
484 void setupDynamicPairlistPruning(const gmx::MDLogger &mdlog,
485 const t_inputrec *ir,
486 const gmx_mtop_t *mtop,
488 const interaction_const_t *ic,
489 PairlistParams *listParams)
491 GMX_RELEASE_ASSERT(listParams->rlistOuter > 0, "With the nbnxn setup rlist should be > 0");
493 /* Initialize the parameters to no dynamic list pruning */
494 listParams->useDynamicPruning = false;
496 const VerletbufListSetup ls =
498 IClusterSizePerListType[listParams->pairlistType],
499 JClusterSizePerListType[listParams->pairlistType]
502 /* Currently emulation mode does not support dual pair-lists */
503 const bool useGpuList = (listParams->pairlistType == PairlistType::HierarchicalNxN);
505 if (supportsDynamicPairlistGenerationInterval(*ir) &&
506 getenv("GMX_DISABLE_DYNAMICPRUNING") == nullptr)
508 /* Note that nstlistPrune can have any value independently of nstlist.
509 * Actually applying rolling pruning is only useful when
510 * nstlistPrune < nstlist -1
512 char *env = getenv("GMX_NSTLIST_DYNAMICPRUNING");
513 bool userSetNstlistPrune = (env != nullptr);
515 if (userSetNstlistPrune)
518 listParams->nstlistPrune = strtol(env, &end, 10);
519 if (!end || (*end != 0) ||
520 !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < ir->nstlist))
522 gmx_fatal(FARGS, "Invalid value passed in GMX_NSTLIST_DYNAMICPRUNING=%s, should be > 0 and < nstlist", env);
527 static_assert(c_nbnxnDynamicListPruningMinLifetime % c_nbnxnGpuRollingListPruningInterval == 0,
528 "c_nbnxnDynamicListPruningMinLifetime sets the starting value for nstlistPrune, which should be divisible by the rolling pruning interval for efficiency reasons.");
530 // TODO: Use auto-tuning to determine nstlistPrune
531 listParams->nstlistPrune = c_nbnxnDynamicListPruningMinLifetime;
534 setDynamicPairlistPruningParameters(ir, mtop, box, useGpuList, ls,
535 userSetNstlistPrune, ic,
538 if (listParams->useDynamicPruning && useGpuList)
540 /* Note that we can round down here. This makes the effective
541 * rolling pruning interval slightly shorter than nstlistTune,
542 * thus giving correct results, but a slightly lower efficiency.
544 GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval,
545 ( "With dynamic list pruning on GPUs pruning frequency must be at least as large as the rolling pruning interval (" +
546 std::to_string(c_nbnxnGpuRollingListPruningInterval) +
548 listParams->numRollingPruningParts = listParams->nstlistPrune/c_nbnxnGpuRollingListPruningInterval;
552 listParams->numRollingPruningParts = 1;
558 const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
559 if (listParams->useDynamicPruning)
561 mesg += gmx::formatString("Using a dual %dx%d pair-list setup updated with dynamic%s pruning:\n",
562 ls.cluster_size_i, ls.cluster_size_j,
563 listParams->numRollingPruningParts > 1 ? ", rolling" : "");
564 mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
565 mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, listParams->rlistInner, interactionCutoff);
569 mesg += gmx::formatString("Using a %dx%d pair-list setup:\n",
570 ls.cluster_size_i, ls.cluster_size_j);
571 mesg += formatListSetup("", ir->nstlist, ir->nstlist, listParams->rlistOuter, interactionCutoff);
573 if (supportsDynamicPairlistGenerationInterval(*ir))
575 const VerletbufListSetup listSetup1x1 = { 1, 1 };
576 const real rlistOuter =
577 calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
579 real rlistInner = rlistOuter;
580 if (listParams->useDynamicPruning)
582 int listLifeTime = listParams->nstlistPrune - (useGpuList ? 0 : 1);
584 calcVerletBufferSize(*mtop, det(box), *ir, listParams->nstlistPrune, listLifeTime,
588 mesg += gmx::formatString("At tolerance %g kJ/mol/ps per atom, equivalent classical 1x1 list would be:\n",
590 if (listParams->useDynamicPruning)
592 mesg += formatListSetup("outer", ir->nstlist, ir->nstlist, rlistOuter, interactionCutoff);
593 mesg += formatListSetup("inner", listParams->nstlistPrune, ir->nstlist, rlistInner, interactionCutoff);
597 mesg += formatListSetup("", ir->nstlist, ir->nstlist, rlistOuter, interactionCutoff);
601 GMX_LOG(mdlog.info).asParagraph().appendText(mesg);