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48 #include "gmx_fatal.h"
52 #include "types/nb_verlet.h"
53 #include "types/interaction_const.h"
54 #include "types/force_flags.h"
55 #include "../nbnxn_consts.h"
57 #include "nbnxn_cuda_types.h"
58 #include "../../gmxlib/cuda_tools/cudautils.cuh"
59 #include "nbnxn_cuda_data_mgmt.h"
60 #include "pmalloc_cuda.h"
61 #include "gpu_utils.h"
63 static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
65 /* This is a heuristically determined parameter for the Fermi architecture for
66 * the minimum size of ci lists by multiplying this constant with the # of
67 * multiprocessors on the current device.
69 static unsigned int gpu_min_ci_balanced_factor = 40;
71 /* Functions from nbnxn_cuda.cu */
72 extern void nbnxn_cuda_set_cacheconfig(cuda_dev_info_t *devinfo);
73 extern const struct texture<float, 1, cudaReadModeElementType>& nbnxn_cuda_get_nbfp_texref();
74 extern const struct texture<float, 1, cudaReadModeElementType>& nbnxn_cuda_get_coulomb_tab_texref();
76 /* We should actually be using md_print_warn in md_logging.c,
77 * but we can't include mpi.h in CUDA code.
79 static void md_print_warn(FILE *fplog,
86 /* We should only print to stderr on the master node,
87 * in most cases fplog is only set on the master node, so this works.
90 fprintf(stderr, "\n");
91 vfprintf(stderr, fmt, ap);
92 fprintf(stderr, "\n");
97 vfprintf(fplog, fmt, ap);
105 static void nbnxn_cuda_clear_e_fshift(nbnxn_cuda_ptr_t cu_nb);
108 /*! Tabulates the Ewald Coulomb force and initializes the size/scale
109 and the table GPU array. If called with an already allocated table,
110 it just re-uploads the table.
112 static void init_ewald_coulomb_force_table(cu_nbparam_t *nbp)
114 float *ftmp, *coul_tab;
119 tabsize = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
120 /* Subtract 2 iso 1 to avoid access out of range due to rounding */
121 tabscale = (tabsize - 2) / sqrt(nbp->rcoulomb_sq);
123 pmalloc((void**)&ftmp, tabsize*sizeof(*ftmp));
125 table_spline3_fill_ewald_lr(ftmp, NULL, NULL, tabsize,
126 1/tabscale, nbp->ewald_beta);
128 /* If the table pointer == NULL the table is generated the first time =>
129 the array pointer will be saved to nbparam and the texture is bound.
131 coul_tab = nbp->coulomb_tab;
132 if (coul_tab == NULL)
134 stat = cudaMalloc((void **)&coul_tab, tabsize*sizeof(*coul_tab));
135 CU_RET_ERR(stat, "cudaMalloc failed on coul_tab");
137 nbp->coulomb_tab = coul_tab;
139 cudaChannelFormatDesc cd = cudaCreateChannelDesc<float>();
140 stat = cudaBindTexture(NULL, &nbnxn_cuda_get_coulomb_tab_texref(),
141 coul_tab, &cd, tabsize*sizeof(*coul_tab));
142 CU_RET_ERR(stat, "cudaBindTexture on coul_tab failed");
145 cu_copy_H2D(coul_tab, ftmp, tabsize*sizeof(*coul_tab));
147 nbp->coulomb_tab_size = tabsize;
148 nbp->coulomb_tab_scale = tabscale;
154 /*! Initializes the atomdata structure first time, it only gets filled at
156 static void init_atomdata_first(cu_atomdata_t *ad, int ntypes)
161 stat = cudaMalloc((void**)&ad->shift_vec, SHIFTS*sizeof(*ad->shift_vec));
162 CU_RET_ERR(stat, "cudaMalloc failed on ad->shift_vec");
163 ad->bShiftVecUploaded = false;
165 stat = cudaMalloc((void**)&ad->fshift, SHIFTS*sizeof(*ad->fshift));
166 CU_RET_ERR(stat, "cudaMalloc failed on ad->fshift");
168 stat = cudaMalloc((void**)&ad->e_lj, sizeof(*ad->e_lj));
169 CU_RET_ERR(stat, "cudaMalloc failed on ad->e_lj");
170 stat = cudaMalloc((void**)&ad->e_el, sizeof(*ad->e_el));
171 CU_RET_ERR(stat, "cudaMalloc failed on ad->e_el");
173 /* initialize to NULL poiters to data that is not allocated here and will
174 need reallocation in nbnxn_cuda_init_atomdata */
178 /* size -1 indicates that the respective array hasn't been initialized yet */
183 /*! Selects the Ewald kernel type, analytical on SM 3.0 and later, tabulated on
184 earlier GPUs, single or twin cut-off. */
185 static int pick_ewald_kernel_type(bool bTwinCut,
186 const cuda_dev_info_t *dev_info)
188 bool bUseAnalyticalEwald, bForceAnalyticalEwald, bForceTabulatedEwald;
191 /* Benchmarking/development environment variables to force the use of
192 analytical or tabulated Ewald kernel. */
193 bForceAnalyticalEwald = (getenv("GMX_CUDA_NB_ANA_EWALD") != NULL);
194 bForceTabulatedEwald = (getenv("GMX_CUDA_NB_TAB_EWALD") != NULL);
196 if (bForceAnalyticalEwald && bForceTabulatedEwald)
198 gmx_incons("Both analytical and tabulated Ewald CUDA non-bonded kernels "
199 "requested through environment variables.");
202 /* By default, on SM 3.0 and later use analytical Ewald, on earlier tabulated. */
203 if ((dev_info->prop.major >= 3 || bForceAnalyticalEwald) && !bForceTabulatedEwald)
205 bUseAnalyticalEwald = true;
209 fprintf(debug, "Using analytical Ewald CUDA kernels\n");
214 bUseAnalyticalEwald = false;
218 fprintf(debug, "Using tabulated Ewald CUDA kernels\n");
222 /* Use twin cut-off kernels if requested by bTwinCut or the env. var.
223 forces it (use it for debugging/benchmarking only). */
224 if (!bTwinCut && (getenv("GMX_CUDA_NB_EWALD_TWINCUT") == NULL))
226 kernel_type = bUseAnalyticalEwald ? eelCuEWALD_ANA : eelCuEWALD_TAB;
230 kernel_type = bUseAnalyticalEwald ? eelCuEWALD_ANA_TWIN : eelCuEWALD_TAB_TWIN;
237 /*! Initializes the nonbonded parameter data structure. */
238 static void init_nbparam(cu_nbparam_t *nbp,
239 const interaction_const_t *ic,
240 const nbnxn_atomdata_t *nbat,
241 const cuda_dev_info_t *dev_info)
246 ntypes = nbat->ntype;
248 nbp->ewald_beta = ic->ewaldcoeff;
249 nbp->sh_ewald = ic->sh_ewald;
250 nbp->epsfac = ic->epsfac;
251 nbp->two_k_rf = 2.0 * ic->k_rf;
252 nbp->c_rf = ic->c_rf;
253 nbp->rvdw_sq = ic->rvdw * ic->rvdw;
254 nbp->rcoulomb_sq= ic->rcoulomb * ic->rcoulomb;
255 nbp->rlist_sq = ic->rlist * ic->rlist;
256 nbp->sh_invrc6 = ic->sh_invrc6;
258 if (ic->eeltype == eelCUT)
260 nbp->eeltype = eelCuCUT;
262 else if (EEL_RF(ic->eeltype))
264 nbp->eeltype = eelCuRF;
266 else if ((EEL_PME(ic->eeltype) || ic->eeltype==eelEWALD))
268 /* Initially rcoulomb == rvdw, so it's surely not twin cut-off. */
269 nbp->eeltype = pick_ewald_kernel_type(false, dev_info);
273 /* Shouldn't happen, as this is checked when choosing Verlet-scheme */
274 gmx_incons("The requested electrostatics type is not implemented in the CUDA GPU accelerated kernels!");
277 /* generate table for PME */
278 nbp->coulomb_tab = NULL;
279 if (nbp->eeltype == eelCuEWALD_TAB || nbp->eeltype == eelCuEWALD_TAB_TWIN)
281 init_ewald_coulomb_force_table(nbp);
284 nnbfp = 2*ntypes*ntypes;
285 stat = cudaMalloc((void **)&nbp->nbfp, nnbfp*sizeof(*nbp->nbfp));
286 CU_RET_ERR(stat, "cudaMalloc failed on nbp->nbfp");
287 cu_copy_H2D(nbp->nbfp, nbat->nbfp, nnbfp*sizeof(*nbp->nbfp));
289 cudaChannelFormatDesc cd = cudaCreateChannelDesc<float>();
290 stat = cudaBindTexture(NULL, &nbnxn_cuda_get_nbfp_texref(),
291 nbp->nbfp, &cd, nnbfp*sizeof(*nbp->nbfp));
292 CU_RET_ERR(stat, "cudaBindTexture on nbfp failed");
295 /*! Re-generate the GPU Ewald force table, resets rlist, and update the
296 * electrostatic type switching to twin cut-off (or back) if needed. */
297 void nbnxn_cuda_pme_loadbal_update_param(nbnxn_cuda_ptr_t cu_nb,
298 const interaction_const_t *ic)
300 cu_nbparam_t *nbp = cu_nb->nbparam;
302 nbp->rlist_sq = ic->rlist * ic->rlist;
303 nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
304 nbp->ewald_beta = ic->ewaldcoeff;
306 nbp->eeltype = pick_ewald_kernel_type(ic->rcoulomb != ic->rvdw,
309 init_ewald_coulomb_force_table(cu_nb->nbparam);
312 /*! Initializes the pair list data structure. */
313 static void init_plist(cu_plist_t *pl)
315 /* initialize to NULL pointers to data that is not allocated here and will
316 need reallocation in nbnxn_cuda_init_pairlist */
321 /* size -1 indicates that the respective array hasn't been initialized yet */
328 pl->excl_nalloc = -1;
329 pl->bDoPrune = false;
332 /*! Initializes the timer data structure. */
333 static void init_timers(cu_timers_t *t, bool bUseTwoStreams)
336 int eventflags = ( bUseCudaEventBlockingSync ? cudaEventBlockingSync: cudaEventDefault );
338 stat = cudaEventCreateWithFlags(&(t->start_atdat), eventflags);
339 CU_RET_ERR(stat, "cudaEventCreate on start_atdat failed");
340 stat = cudaEventCreateWithFlags(&(t->stop_atdat), eventflags);
341 CU_RET_ERR(stat, "cudaEventCreate on stop_atdat failed");
343 /* The non-local counters/stream (second in the array) are needed only with DD. */
344 for (int i = 0; i <= (bUseTwoStreams ? 1 : 0); i++)
346 stat = cudaEventCreateWithFlags(&(t->start_nb_k[i]), eventflags);
347 CU_RET_ERR(stat, "cudaEventCreate on start_nb_k failed");
348 stat = cudaEventCreateWithFlags(&(t->stop_nb_k[i]), eventflags);
349 CU_RET_ERR(stat, "cudaEventCreate on stop_nb_k failed");
352 stat = cudaEventCreateWithFlags(&(t->start_pl_h2d[i]), eventflags);
353 CU_RET_ERR(stat, "cudaEventCreate on start_pl_h2d failed");
354 stat = cudaEventCreateWithFlags(&(t->stop_pl_h2d[i]), eventflags);
355 CU_RET_ERR(stat, "cudaEventCreate on stop_pl_h2d failed");
357 stat = cudaEventCreateWithFlags(&(t->start_nb_h2d[i]), eventflags);
358 CU_RET_ERR(stat, "cudaEventCreate on start_nb_h2d failed");
359 stat = cudaEventCreateWithFlags(&(t->stop_nb_h2d[i]), eventflags);
360 CU_RET_ERR(stat, "cudaEventCreate on stop_nb_h2d failed");
362 stat = cudaEventCreateWithFlags(&(t->start_nb_d2h[i]), eventflags);
363 CU_RET_ERR(stat, "cudaEventCreate on start_nb_d2h failed");
364 stat = cudaEventCreateWithFlags(&(t->stop_nb_d2h[i]), eventflags);
365 CU_RET_ERR(stat, "cudaEventCreate on stop_nb_d2h failed");
369 /*! Initializes the timings data structure. */
370 static void init_timings(wallclock_gpu_t *t)
379 for (i = 0; i < 2; i++)
381 for(j = 0; j < 2; j++)
383 t->ktime[i][j].t = 0.0;
384 t->ktime[i][j].c = 0;
389 /* Decide which kernel version to use (default or legacy) based on:
390 * - CUDA version used for compilation
391 * - non-bonded kernel selector environment variables
392 * - GPU architecture version
394 static int pick_nbnxn_kernel_version(FILE *fplog,
395 cuda_dev_info_t *devinfo)
397 bool bForceLegacyKernel, bForceDefaultKernel, bCUDA40, bCUDA32;
401 /* Legacy kernel (former k2), kept for backward compatibility as it is
402 faster than the default with CUDA 3.2/4.0 on Fermi (not on Kepler). */
403 bForceLegacyKernel = (getenv("GMX_CUDA_NB_LEGACY") != NULL);
404 /* default kernel (former k3). */
405 bForceDefaultKernel = (getenv("GMX_CUDA_NB_DEFAULT") != NULL);
407 if ((unsigned)(bForceLegacyKernel + bForceDefaultKernel) > 1)
409 gmx_fatal(FARGS, "Multiple CUDA non-bonded kernels requested; to manually pick a kernel set only one \n"
410 "of the following environment variables: \n"
411 "GMX_CUDA_NB_DEFAULT, GMX_CUDA_NB_LEGACY");
414 bCUDA32 = bCUDA40 = false;
415 #if CUDA_VERSION == 3200
417 sprintf(sbuf, "3.2");
418 #elif CUDA_VERSION == 4000
420 sprintf(sbuf, "4.0");
423 /* default is default ;) */
424 kver = eNbnxnCuKDefault;
426 /* Consider switching to legacy kernels only on Fermi */
427 if (devinfo->prop.major < 3 && (bCUDA32 || bCUDA40))
429 /* use legacy kernel unless something else is forced by an env. var */
430 if (bForceDefaultKernel)
433 "NOTE: CUDA %s compilation detected; with this compiler version the legacy\n"
434 " non-bonded kernels perform best. However, the default kernels were\n"
435 " selected by the GMX_CUDA_NB_DEFAULT environment variable.\n"
436 " For best performance upgrade your CUDA toolkit.\n",
441 kver = eNbnxnCuKLegacy;
446 /* issue note if the non-default kernel is forced by an env. var */
447 if (bForceLegacyKernel)
450 "NOTE: Legacy non-bonded CUDA kernels selected by the GMX_CUDA_NB_LEGACY\n"
451 " env. var. Consider using using the default kernels which should be faster!\n");
453 kver = eNbnxnCuKLegacy;
460 void nbnxn_cuda_init(FILE *fplog,
461 nbnxn_cuda_ptr_t *p_cu_nb,
462 gmx_gpu_info_t *gpu_info, int my_gpu_index,
463 gmx_bool bLocalAndNonlocal)
468 bool bStreamSync, bNoStreamSync, bTMPIAtomics, bX86, bOldDriver;
473 if (p_cu_nb == NULL) return;
477 snew(nb->nbparam, 1);
478 snew(nb->plist[eintLocal], 1);
479 if (bLocalAndNonlocal)
481 snew(nb->plist[eintNonlocal], 1);
484 nb->bUseTwoStreams = bLocalAndNonlocal;
487 snew(nb->timings, 1);
490 pmalloc((void**)&nb->nbst.e_lj, sizeof(*nb->nbst.e_lj));
491 pmalloc((void**)&nb->nbst.e_el, sizeof(*nb->nbst.e_el));
492 pmalloc((void**)&nb->nbst.fshift, SHIFTS * sizeof(*nb->nbst.fshift));
494 init_plist(nb->plist[eintLocal]);
496 /* local/non-local GPU streams */
497 stat = cudaStreamCreate(&nb->stream[eintLocal]);
498 CU_RET_ERR(stat, "cudaStreamCreate on stream[eintLocal] failed");
499 if (nb->bUseTwoStreams)
501 init_plist(nb->plist[eintNonlocal]);
502 stat = cudaStreamCreate(&nb->stream[eintNonlocal]);
503 CU_RET_ERR(stat, "cudaStreamCreate on stream[eintNonlocal] failed");
506 /* init events for sychronization (timing disabled for performance reasons!) */
507 stat = cudaEventCreateWithFlags(&nb->nonlocal_done, cudaEventDisableTiming);
508 CU_RET_ERR(stat, "cudaEventCreate on nonlocal_done failed");
509 stat = cudaEventCreateWithFlags(&nb->misc_ops_done, cudaEventDisableTiming);
510 CU_RET_ERR(stat, "cudaEventCreate on misc_ops_one failed");
512 /* set device info, just point it to the right GPU among the detected ones */
513 nb->dev_info = &gpu_info->cuda_dev[get_gpu_device_id(gpu_info, my_gpu_index)];
515 /* On GPUs with ECC enabled, cudaStreamSynchronize shows a large overhead
516 * (which increases with shorter time/step) caused by a known CUDA driver bug.
517 * To work around the issue we'll use an (admittedly fragile) memory polling
518 * waiting to preserve performance. This requires support for atomic
519 * operations and only works on x86/x86_64.
520 * With polling wait event-timing also needs to be disabled.
522 * The overhead is greatly reduced in API v5.0 drivers and the improvement
523 $ is independent of runtime version. Hence, with API v5.0 drivers and later
524 * we won't switch to polling.
526 * NOTE: Unfortunately, this is known to fail when GPUs are shared by (t)MPI,
527 * ranks so we will also disable it in that case.
530 bStreamSync = getenv("GMX_CUDA_STREAMSYNC") != NULL;
531 bNoStreamSync = getenv("GMX_NO_CUDA_STREAMSYNC") != NULL;
536 bTMPIAtomics = false;
539 #if defined(i386) || defined(__x86_64__)
545 if (bStreamSync && bNoStreamSync)
547 gmx_fatal(FARGS, "Conflicting environment variables: both GMX_CUDA_STREAMSYNC and GMX_NO_CUDA_STREAMSYNC defined");
550 stat = cudaDriverGetVersion(&cuda_drv_ver);
551 CU_RET_ERR(stat, "cudaDriverGetVersion failed");
553 bOldDriver = (cuda_drv_ver < 5000);
555 if ((nb->dev_info->prop.ECCEnabled == 1) && bOldDriver)
557 /* Polling wait should be used instead of cudaStreamSynchronize only if:
558 * - ECC is ON & driver is old (checked above),
559 * - we're on x86/x86_64,
560 * - atomics are available, and
561 * - GPUs are not being shared.
563 bool bShouldUsePollSync = (bX86 && bTMPIAtomics && !gpu_info->bDevShare);
567 nb->bUseStreamSync = true;
569 /* only warn if polling should be used */
570 if (bShouldUsePollSync)
573 "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, but\n"
574 " cudaStreamSynchronize waiting is forced by the GMX_CUDA_STREAMSYNC env. var.\n");
579 nb->bUseStreamSync = !bShouldUsePollSync;
581 if (bShouldUsePollSync)
584 "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0, known to\n"
585 " cause performance loss. Switching to the alternative polling GPU wait.\n"
586 " If you encounter issues, switch back to standard GPU waiting by setting\n"
587 " the GMX_CUDA_STREAMSYNC environment variable.\n");
591 /* Tell the user that the ECC+old driver combination can be bad */
593 "NOTE: Using a GPU with ECC enabled and CUDA driver API version <5.0.\n"
594 " A known bug in this driver version can cause performance loss.\n"
595 " However, the polling wait workaround can not be used because\n%s\n"
596 " Consider updating the driver or turning ECC off.",
597 (bX86 && bTMPIAtomics) ?
598 " GPU(s) are being oversubscribed." :
599 " atomic operations are not supported by the platform/CPU+compiler.");
600 md_print_warn(fplog, sbuf);
608 nb->bUseStreamSync = false;
611 "NOTE: Polling wait for GPU synchronization requested by GMX_NO_CUDA_STREAMSYNC\n");
615 /* no/off ECC, cudaStreamSynchronize not turned off by env. var. */
616 nb->bUseStreamSync = true;
620 /* CUDA timing disabled as event timers don't work:
621 - with multiple streams = domain-decomposition;
622 - with the polling waiting hack (without cudaStreamSynchronize);
623 - when turned off by GMX_DISABLE_CUDA_TIMING.
625 nb->bDoTime = (!nb->bUseTwoStreams && nb->bUseStreamSync &&
626 (getenv("GMX_DISABLE_CUDA_TIMING") == NULL));
630 init_timers(nb->timers, nb->bUseTwoStreams);
631 init_timings(nb->timings);
634 /* set the kernel type for the current GPU */
635 nb->kernel_ver = pick_nbnxn_kernel_version(fplog, nb->dev_info);
636 /* pick L1 cache configuration */
637 nbnxn_cuda_set_cacheconfig(nb->dev_info);
643 fprintf(debug, "Initialized CUDA data structures.\n");
647 void nbnxn_cuda_init_const(nbnxn_cuda_ptr_t cu_nb,
648 const interaction_const_t *ic,
649 const nonbonded_verlet_group_t *nbv_group)
651 init_atomdata_first(cu_nb->atdat, nbv_group[0].nbat->ntype);
652 init_nbparam(cu_nb->nbparam, ic, nbv_group[0].nbat, cu_nb->dev_info);
654 /* clear energy and shift force outputs */
655 nbnxn_cuda_clear_e_fshift(cu_nb);
658 void nbnxn_cuda_init_pairlist(nbnxn_cuda_ptr_t cu_nb,
659 const nbnxn_pairlist_t *h_plist,
664 bool bDoTime = cu_nb->bDoTime;
665 cudaStream_t stream = cu_nb->stream[iloc];
666 cu_plist_t *d_plist = cu_nb->plist[iloc];
668 if (d_plist->na_c < 0)
670 d_plist->na_c = h_plist->na_ci;
674 if (d_plist->na_c != h_plist->na_ci)
676 sprintf(sbuf, "In cu_init_plist: the #atoms per cell has changed (from %d to %d)",
677 d_plist->na_c, h_plist->na_ci);
684 stat = cudaEventRecord(cu_nb->timers->start_pl_h2d[iloc], stream);
685 CU_RET_ERR(stat, "cudaEventRecord failed");
688 cu_realloc_buffered((void **)&d_plist->sci, h_plist->sci, sizeof(*d_plist->sci),
689 &d_plist->nsci, &d_plist->sci_nalloc,
693 cu_realloc_buffered((void **)&d_plist->cj4, h_plist->cj4, sizeof(*d_plist->cj4),
694 &d_plist->ncj4, &d_plist->cj4_nalloc,
698 cu_realloc_buffered((void **)&d_plist->excl, h_plist->excl, sizeof(*d_plist->excl),
699 &d_plist->nexcl, &d_plist->excl_nalloc,
705 stat = cudaEventRecord(cu_nb->timers->stop_pl_h2d[iloc], stream);
706 CU_RET_ERR(stat, "cudaEventRecord failed");
709 /* need to prune the pair list during the next step */
710 d_plist->bDoPrune = true;
713 void nbnxn_cuda_upload_shiftvec(nbnxn_cuda_ptr_t cu_nb,
714 const nbnxn_atomdata_t *nbatom)
716 cu_atomdata_t *adat = cu_nb->atdat;
717 cudaStream_t ls = cu_nb->stream[eintLocal];
719 /* only if we have a dynamic box */
720 if (nbatom->bDynamicBox || !adat->bShiftVecUploaded)
722 cu_copy_H2D_async(adat->shift_vec, nbatom->shift_vec,
723 SHIFTS * sizeof(*adat->shift_vec), ls);
724 adat->bShiftVecUploaded = true;
728 /*! Clears the first natoms_clear elements of the GPU nonbonded force output array. */
729 static void nbnxn_cuda_clear_f(nbnxn_cuda_ptr_t cu_nb, int natoms_clear)
732 cu_atomdata_t *adat = cu_nb->atdat;
733 cudaStream_t ls = cu_nb->stream[eintLocal];
735 stat = cudaMemsetAsync(adat->f, 0, natoms_clear * sizeof(*adat->f), ls);
736 CU_RET_ERR(stat, "cudaMemsetAsync on f falied");
739 /*! Clears nonbonded shift force output array and energy outputs on the GPU. */
740 static void nbnxn_cuda_clear_e_fshift(nbnxn_cuda_ptr_t cu_nb)
743 cu_atomdata_t *adat = cu_nb->atdat;
744 cudaStream_t ls = cu_nb->stream[eintLocal];
746 stat = cudaMemsetAsync(adat->fshift, 0, SHIFTS * sizeof(*adat->fshift), ls);
747 CU_RET_ERR(stat, "cudaMemsetAsync on fshift falied");
748 stat = cudaMemsetAsync(adat->e_lj, 0, sizeof(*adat->e_lj), ls);
749 CU_RET_ERR(stat, "cudaMemsetAsync on e_lj falied");
750 stat = cudaMemsetAsync(adat->e_el, 0, sizeof(*adat->e_el), ls);
751 CU_RET_ERR(stat, "cudaMemsetAsync on e_el falied");
754 void nbnxn_cuda_clear_outputs(nbnxn_cuda_ptr_t cu_nb, int flags)
756 nbnxn_cuda_clear_f(cu_nb, cu_nb->atdat->natoms);
757 /* clear shift force array and energies if the outputs were
758 used in the current step */
759 if (flags & GMX_FORCE_VIRIAL)
761 nbnxn_cuda_clear_e_fshift(cu_nb);
765 void nbnxn_cuda_init_atomdata(nbnxn_cuda_ptr_t cu_nb,
766 const nbnxn_atomdata_t *nbat)
771 bool bDoTime = cu_nb->bDoTime;
772 cu_timers_t *timers = cu_nb->timers;
773 cu_atomdata_t *d_atdat = cu_nb->atdat;
774 cudaStream_t ls = cu_nb->stream[eintLocal];
776 natoms = nbat->natoms;
781 /* time async copy */
782 stat = cudaEventRecord(timers->start_atdat, ls);
783 CU_RET_ERR(stat, "cudaEventRecord failed");
786 /* need to reallocate if we have to copy more atoms than the amount of space
787 available and only allocate if we haven't initialized yet, i.e d_atdat->natoms == -1 */
788 if (natoms > d_atdat->nalloc)
790 nalloc = over_alloc_small(natoms);
792 /* free up first if the arrays have already been initialized */
793 if (d_atdat->nalloc != -1)
795 cu_free_buffered(d_atdat->f, &d_atdat->natoms, &d_atdat->nalloc);
796 cu_free_buffered(d_atdat->xq);
797 cu_free_buffered(d_atdat->atom_types);
800 stat = cudaMalloc((void **)&d_atdat->f, nalloc*sizeof(*d_atdat->f));
801 CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->f");
802 stat = cudaMalloc((void **)&d_atdat->xq, nalloc*sizeof(*d_atdat->xq));
803 CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->xq");
805 stat = cudaMalloc((void **)&d_atdat->atom_types, nalloc*sizeof(*d_atdat->atom_types));
806 CU_RET_ERR(stat, "cudaMalloc failed on d_atdat->atom_types");
808 d_atdat->nalloc = nalloc;
812 d_atdat->natoms = natoms;
813 d_atdat->natoms_local = nbat->natoms_local;
815 /* need to clear GPU f output if realloc happened */
818 nbnxn_cuda_clear_f(cu_nb, nalloc);
821 cu_copy_H2D_async(d_atdat->atom_types, nbat->type,
822 natoms*sizeof(*d_atdat->atom_types), ls);
826 stat = cudaEventRecord(timers->stop_atdat, ls);
827 CU_RET_ERR(stat, "cudaEventRecord failed");
831 void nbnxn_cuda_free(FILE *fplog, nbnxn_cuda_ptr_t cu_nb)
834 cu_atomdata_t *atdat;
835 cu_nbparam_t *nbparam;
836 cu_plist_t *plist, *plist_nl;
839 if (cu_nb == NULL) return;
841 atdat = cu_nb->atdat;
842 nbparam = cu_nb->nbparam;
843 plist = cu_nb->plist[eintLocal];
844 plist_nl = cu_nb->plist[eintNonlocal];
845 timers = cu_nb->timers;
847 if (nbparam->eeltype == eelCuEWALD_TAB || nbparam->eeltype == eelCuEWALD_TAB_TWIN)
849 stat = cudaUnbindTexture(nbnxn_cuda_get_coulomb_tab_texref());
850 CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab failed");
851 cu_free_buffered(nbparam->coulomb_tab, &nbparam->coulomb_tab_size);
854 stat = cudaEventDestroy(cu_nb->nonlocal_done);
855 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->nonlocal_done");
856 stat = cudaEventDestroy(cu_nb->misc_ops_done);
857 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->misc_ops_done");
861 stat = cudaEventDestroy(timers->start_atdat);
862 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_atdat");
863 stat = cudaEventDestroy(timers->stop_atdat);
864 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_atdat");
866 /* The non-local counters/stream (second in the array) are needed only with DD. */
867 for (int i = 0; i <= (cu_nb->bUseTwoStreams ? 1 : 0); i++)
869 stat = cudaEventDestroy(timers->start_nb_k[i]);
870 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_k");
871 stat = cudaEventDestroy(timers->stop_nb_k[i]);
872 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_k");
874 stat = cudaEventDestroy(timers->start_pl_h2d[i]);
875 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_pl_h2d");
876 stat = cudaEventDestroy(timers->stop_pl_h2d[i]);
877 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_pl_h2d");
879 stat = cudaStreamDestroy(cu_nb->stream[i]);
880 CU_RET_ERR(stat, "cudaStreamDestroy failed on stream");
882 stat = cudaEventDestroy(timers->start_nb_h2d[i]);
883 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_h2d");
884 stat = cudaEventDestroy(timers->stop_nb_h2d[i]);
885 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_h2d");
887 stat = cudaEventDestroy(timers->start_nb_d2h[i]);
888 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_nb_d2h");
889 stat = cudaEventDestroy(timers->stop_nb_d2h[i]);
890 CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_d2h");
894 stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_texref());
895 CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab failed");
896 cu_free_buffered(nbparam->nbfp);
898 stat = cudaFree(atdat->shift_vec);
899 CU_RET_ERR(stat, "cudaFree failed on atdat->shift_vec");
900 stat = cudaFree(atdat->fshift);
901 CU_RET_ERR(stat, "cudaFree failed on atdat->fshift");
903 stat = cudaFree(atdat->e_lj);
904 CU_RET_ERR(stat, "cudaFree failed on atdat->e_lj");
905 stat = cudaFree(atdat->e_el);
906 CU_RET_ERR(stat, "cudaFree failed on atdat->e_el");
908 cu_free_buffered(atdat->f, &atdat->natoms, &atdat->nalloc);
909 cu_free_buffered(atdat->xq);
910 cu_free_buffered(atdat->atom_types, &atdat->ntypes);
912 cu_free_buffered(plist->sci, &plist->nsci, &plist->sci_nalloc);
913 cu_free_buffered(plist->cj4, &plist->ncj4, &plist->cj4_nalloc);
914 cu_free_buffered(plist->excl, &plist->nexcl, &plist->excl_nalloc);
915 if (cu_nb->bUseTwoStreams)
917 cu_free_buffered(plist_nl->sci, &plist_nl->nsci, &plist_nl->sci_nalloc);
918 cu_free_buffered(plist_nl->cj4, &plist_nl->ncj4, &plist_nl->cj4_nalloc);
919 cu_free_buffered(plist_nl->excl, &plist_nl->nexcl, &plist->excl_nalloc);
925 if (cu_nb->bUseTwoStreams)
930 sfree(cu_nb->timings);
935 fprintf(debug, "Cleaned up CUDA data structures.\n");
939 void cu_synchstream_atdat(nbnxn_cuda_ptr_t cu_nb, int iloc)
942 cudaStream_t stream = cu_nb->stream[iloc];
944 stat = cudaStreamWaitEvent(stream, cu_nb->timers->stop_atdat, 0);
945 CU_RET_ERR(stat, "cudaStreamWaitEvent failed");
948 wallclock_gpu_t * nbnxn_cuda_get_timings(nbnxn_cuda_ptr_t cu_nb)
950 return (cu_nb != NULL && cu_nb->bDoTime) ? cu_nb->timings : NULL;
953 void nbnxn_cuda_reset_timings(nbnxn_cuda_ptr_t cu_nb)
957 init_timings(cu_nb->timings);
961 int nbnxn_cuda_min_ci_balanced(nbnxn_cuda_ptr_t cu_nb)
963 return cu_nb != NULL ?
964 gpu_min_ci_balanced_factor*cu_nb->dev_info->prop.multiProcessorCount : 0;