{ k_nbnxn_ewald_twin_ener, k_nbnxn_ewald_twin_ener_prune } },
};
-/*! Pointers to the legacy kernels organized in a 3 dim array by:
- * electrostatics type, energy calculation on/off, and pruning on/off.
- *
- * Note that the order of electrostatics (1st dimension) has to match the
- * order of corresponding enumerated types defined in nbnxn_cuda_types.h.
- */
-static const nbnxn_cu_kfunc_ptr_t
-nb_legacy_kfunc_ptr[eelCuNR][nEnergyKernelTypes][nPruneKernelTypes] =
-{
- { { k_nbnxn_cutoff_legacy, k_nbnxn_cutoff_prune_legacy },
- { k_nbnxn_cutoff_ener_legacy, k_nbnxn_cutoff_ener_prune_legacy } },
- { { k_nbnxn_rf_legacy, k_nbnxn_rf_prune_legacy },
- { k_nbnxn_rf_ener_legacy, k_nbnxn_rf_ener_prune_legacy } },
- { { k_nbnxn_ewald_tab_legacy, k_nbnxn_ewald_tab_prune_legacy },
- { k_nbnxn_ewald_tab_ener_legacy, k_nbnxn_ewald_tab_ener_prune_legacy } },
- { { k_nbnxn_ewald_tab_twin_legacy, k_nbnxn_ewald_tab_twin_prune_legacy },
- { k_nbnxn_ewald_tab_twin_ener_legacy, k_nbnxn_ewald_tab_twin_ener_prune_legacy } },
-};
-
/*! Return a pointer to the kernel version to be executed at the current step. */
-static inline nbnxn_cu_kfunc_ptr_t select_nbnxn_kernel(int kver, int eeltype,
- bool bDoEne, bool bDoPrune)
+static inline nbnxn_cu_kfunc_ptr_t select_nbnxn_kernel(int eeltype,
+ bool bDoEne,
+ bool bDoPrune)
{
- assert(kver < eNbnxnCuKNR);
assert(eeltype < eelCuNR);
- if (NBNXN_KVER_LEGACY(kver))
- {
- /* no analytical Ewald with legacy kernels */
- assert(eeltype <= eelCuEWALD_TAB_TWIN);
-
- return nb_legacy_kfunc_ptr[eeltype][bDoEne][bDoPrune];
- }
- else
- {
- return nb_default_kfunc_ptr[eeltype][bDoEne][bDoPrune];
- }
+ return nb_default_kfunc_ptr[eeltype][bDoEne][bDoPrune];
}
-/*! Calculates the amount of shared memory required for kernel version in use. */
-static inline int calc_shmem_required(int kver)
+/*! Calculates the amount of shared memory required by the CUDA kernel in use. */
+static inline int calc_shmem_required()
{
int shmem;
/* size of shmem (force-buffers/xq/atom type preloading) */
- if (NBNXN_KVER_LEGACY(kver))
- {
- /* i-atom x+q in shared memory */
- shmem = NCL_PER_SUPERCL * CL_SIZE * sizeof(float4);
- /* force reduction buffers in shared memory */
- shmem += CL_SIZE * CL_SIZE * 3 * sizeof(float);
- }
- else
- {
- /* NOTE: with the default kernel on sm3.0 we need shmem only for pre-loading */
- /* i-atom x+q in shared memory */
- shmem = NCL_PER_SUPERCL * CL_SIZE * sizeof(float4);
- /* cj in shared memory, for both warps separately */
- shmem += 2 * NBNXN_GPU_JGROUP_SIZE * sizeof(int);
+ /* NOTE: with the default kernel on sm3.0 we need shmem only for pre-loading */
+ /* i-atom x+q in shared memory */
+ shmem = NCL_PER_SUPERCL * CL_SIZE * sizeof(float4);
+ /* cj in shared memory, for both warps separately */
+ shmem += 2 * NBNXN_GPU_JGROUP_SIZE * sizeof(int);
#ifdef IATYPE_SHMEM
- /* i-atom types in shared memory */
- shmem += NCL_PER_SUPERCL * CL_SIZE * sizeof(int);
+ /* i-atom types in shared memory */
+ shmem += NCL_PER_SUPERCL * CL_SIZE * sizeof(int);
#endif
#if __CUDA_ARCH__ < 300
- /* force reduction buffers in shared memory */
- shmem += CL_SIZE * CL_SIZE * 3 * sizeof(float);
+ /* force reduction buffers in shared memory */
+ shmem += CL_SIZE * CL_SIZE * 3 * sizeof(float);
#endif
- }
return shmem;
}
}
/* get the pointer to the kernel flavor we need to use */
- nb_kernel = select_nbnxn_kernel(cu_nb->kernel_ver, nbp->eeltype, bCalcEner,
+ nb_kernel = select_nbnxn_kernel(nbp->eeltype, bCalcEner,
plist->bDoPrune || always_prune);
/* kernel launch config */
nblock = calc_nb_kernel_nblock(plist->nsci, cu_nb->dev_info);
dim_block = dim3(CL_SIZE, CL_SIZE, 1);
dim_grid = dim3(nblock, 1, 1);
- shmem = calc_shmem_required(cu_nb->kernel_ver);
+ shmem = calc_shmem_required();
if (debug)
{
{
for (int k = 0; k < nPruneKernelTypes; k++)
{
- /* Legacy kernel 16/48 kB Shared/L1
- * No analytical Ewald!
- */
- if (i != eelCuEWALD_ANA && i != eelCuEWALD_ANA_TWIN)
- {
- stat = cudaFuncSetCacheConfig(nb_legacy_kfunc_ptr[i][j][k], cudaFuncCachePreferL1);
- CU_RET_ERR(stat, "cudaFuncSetCacheConfig failed");
- }
-
if (devinfo->prop.major >= 3)
{
/* Default kernel on sm 3.x 48/16 kB Shared/L1 */
}
}
-/* Decide which kernel version to use (default or legacy) based on:
- * - CUDA version used for compilation
- * - non-bonded kernel selector environment variables
- * - GPU architecture version
- */
-static int pick_nbnxn_kernel_version(FILE *fplog,
- cuda_dev_info_t *devinfo)
-{
- bool bForceLegacyKernel, bForceDefaultKernel, bCUDA40, bCUDA32;
- char sbuf[STRLEN];
- int kver;
-
- /* Legacy kernel (former k2), kept for backward compatibility as it is
- faster than the default with CUDA 3.2/4.0 on Fermi (not on Kepler). */
- bForceLegacyKernel = (getenv("GMX_CUDA_NB_LEGACY") != NULL);
- /* default kernel (former k3). */
- bForceDefaultKernel = (getenv("GMX_CUDA_NB_DEFAULT") != NULL);
-
- if ((unsigned)(bForceLegacyKernel + bForceDefaultKernel) > 1)
- {
- gmx_fatal(FARGS, "Multiple CUDA non-bonded kernels requested; to manually pick a kernel set only one \n"
- "of the following environment variables: \n"
- "GMX_CUDA_NB_DEFAULT, GMX_CUDA_NB_LEGACY");
- }
-
- bCUDA32 = bCUDA40 = false;
-#if CUDA_VERSION == 3200
- bCUDA32 = true;
- sprintf(sbuf, "3.2");
-#elif CUDA_VERSION == 4000
- bCUDA40 = true;
- sprintf(sbuf, "4.0");
-#endif
-
- /* default is default ;) */
- kver = eNbnxnCuKDefault;
-
- /* Consider switching to legacy kernels only on Fermi */
- if (devinfo->prop.major < 3 && (bCUDA32 || bCUDA40))
- {
- /* use legacy kernel unless something else is forced by an env. var */
- if (bForceDefaultKernel)
- {
- md_print_warn(fplog,
- "NOTE: CUDA %s compilation detected; with this compiler version the legacy\n"
- " non-bonded kernels perform best. However, the default kernels were\n"
- " selected by the GMX_CUDA_NB_DEFAULT environment variable.\n"
- " For best performance upgrade your CUDA toolkit.\n",
- sbuf);
- }
- else
- {
- kver = eNbnxnCuKLegacy;
- }
- }
- else
- {
- /* issue note if the non-default kernel is forced by an env. var */
- if (bForceLegacyKernel)
- {
- md_print_warn(fplog,
- "NOTE: Legacy non-bonded CUDA kernels selected by the GMX_CUDA_NB_LEGACY\n"
- " env. var. Consider using using the default kernels which should be faster!\n");
-
- kver = eNbnxnCuKLegacy;
- }
- }
-
- return kver;
-}
-
void nbnxn_cuda_init(FILE *fplog,
nbnxn_cuda_ptr_t *p_cu_nb,
const gmx_gpu_info_t *gpu_info,
}
/* set the kernel type for the current GPU */
- nb->kernel_ver = pick_nbnxn_kernel_version(fplog, nb->dev_info);
/* pick L1 cache configuration */
nbnxn_cuda_set_cacheconfig(nb->dev_info);
+++ /dev/null
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2012, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
- */
-
-#include "maths.h"
-/* Note that floating-point constants in CUDA code should be suffixed
- * with f (e.g. 0.5f), to stop the compiler producing intermediate
- * code that is in double precision.
- */
-
-/* Analytical Ewald is not implemented for the legacy kernels (as it is anyway
- slower than the tabulated kernel on Fermi). */
-#ifdef EL_EWALD_ANA
-#error Trying to generate Analytical Ewald legacy kernels which is not implemented in the legacy kernels!
-#endif
-
-/*
- Kernel launch parameters:
- - #blocks = #pair lists, blockId = pair list Id
- - #threads = CL_SIZE^2
- - shmem = CL_SIZE^2 * sizeof(float)
-
- Each thread calculates an i force-component taking one pair of i-j atoms.
- */
-#if __CUDA_ARCH__ >= 350
-__launch_bounds__(64,16)
-#endif
-#ifdef PRUNE_NBL
-#ifdef CALC_ENERGIES
-__global__ void NB_KERNEL_FUNC_NAME(k_nbnxn, _ener_prune_legacy)
-#else
-__global__ void NB_KERNEL_FUNC_NAME(k_nbnxn, _prune_legacy)
-#endif
-#else
-#ifdef CALC_ENERGIES
-__global__ void NB_KERNEL_FUNC_NAME(k_nbnxn, _ener_legacy)
-#else
-__global__ void NB_KERNEL_FUNC_NAME(k_nbnxn, _legacy)
-#endif
-#endif
- (const cu_atomdata_t atdat,
- const cu_nbparam_t nbparam,
- const cu_plist_t plist,
- bool bCalcFshift)
-{
- /* convenience variables */
- const nbnxn_sci_t *pl_sci = plist.sci;
-#ifndef PRUNE_NBL
- const
-#endif
- nbnxn_cj4_t *pl_cj4 = plist.cj4;
- const nbnxn_excl_t *excl = plist.excl;
- const int *atom_types = atdat.atom_types;
- int ntypes = atdat.ntypes;
- const float4 *xq = atdat.xq;
- float3 *f = atdat.f;
- const float3 *shift_vec = atdat.shift_vec;
- float rcoulomb_sq = nbparam.rcoulomb_sq;
-#ifdef VDW_CUTOFF_CHECK
- float rvdw_sq = nbparam.rvdw_sq;
- float vdw_in_range;
-#endif
-#ifdef EL_RF
- float two_k_rf = nbparam.two_k_rf;
-#endif
-#ifdef EL_EWALD_TAB
- float coulomb_tab_scale = nbparam.coulomb_tab_scale;
-#endif
-#ifdef PRUNE_NBL
- float rlist_sq = nbparam.rlist_sq;
-#endif
-
-#ifdef CALC_ENERGIES
- float lj_shift = nbparam.sh_invrc6;
-#ifdef EL_EWALD_TAB
- float beta = nbparam.ewald_beta;
- float ewald_shift = nbparam.sh_ewald;
-#else
- float c_rf = nbparam.c_rf;
-#endif
- float *e_lj = atdat.e_lj;
- float *e_el = atdat.e_el;
-#endif
-
- /* thread/block/warp id-s */
- unsigned int tidxi = threadIdx.x;
- unsigned int tidxj = threadIdx.y;
- unsigned int tidx = threadIdx.y * blockDim.x + threadIdx.x;
- unsigned int bidx = blockIdx.x;
- unsigned int widx = tidx / WARP_SIZE; /* warp index */
-
- int sci, ci, cj, ci_offset,
- ai, aj,
- cij4_start, cij4_end,
- typei, typej,
- i, cii, jm, j4, nsubi, wexcl_idx;
- float qi, qj_f,
- r2, inv_r, inv_r2, inv_r6,
- c6, c12,
- int_bit,
-#ifdef CALC_ENERGIES
- E_lj, E_el, E_lj_p,
-#endif
- F_invr;
- unsigned int wexcl, imask, mask_ji;
- float4 xqbuf;
- float3 xi, xj, rv, f_ij, fcj_buf, fshift_buf;
- float3 fci_buf[NCL_PER_SUPERCL]; /* i force buffer */
- nbnxn_sci_t nb_sci;
-
- /* shmem buffer for i x+q pre-loading */
- extern __shared__ float4 xqib[];
- /* shmem j force buffer */
- float *f_buf = (float *)(xqib + NCL_PER_SUPERCL * CL_SIZE);
-
- nb_sci = pl_sci[bidx]; /* my i super-cluster's index = current bidx */
- sci = nb_sci.sci; /* super-cluster */
- cij4_start = nb_sci.cj4_ind_start; /* first ...*/
- cij4_end = nb_sci.cj4_ind_end; /* and last index of j clusters */
-
- /* Store the i-atom x and q in shared memory */
- /* Note: the thread indexing here is inverted with respect to the
- inner-loop as this results in slightly higher performance */
- ci = sci * NCL_PER_SUPERCL + tidxi;
- ai = ci * CL_SIZE + tidxj;
- xqib[tidxi * CL_SIZE + tidxj] = xq[ai] + shift_vec[nb_sci.shift];
- __syncthreads();
-
- for(ci_offset = 0; ci_offset < NCL_PER_SUPERCL; ci_offset++)
- {
- fci_buf[ci_offset] = make_float3(0.0f);
- }
-
-#ifdef CALC_ENERGIES
- E_lj = 0.0f;
- E_el = 0.0f;
-
-#if defined EL_EWALD_TAB || defined EL_RF
- if (nb_sci.shift == CENTRAL && pl_cj4[cij4_start].cj[0] == sci*NCL_PER_SUPERCL)
- {
- /* we have the diagonal: add the charge self interaction energy term */
- for (i = 0; i < NCL_PER_SUPERCL; i++)
- {
- qi = xqib[i * CL_SIZE + tidxi].w;
- E_el += qi*qi;
- }
- /* divide the self term equally over the j-threads */
- E_el /= CL_SIZE;
-#ifdef EL_RF
- E_el *= -nbparam.epsfac*0.5f*c_rf;
-#else
- E_el *= -nbparam.epsfac*beta*M_FLOAT_1_SQRTPI; /* last factor 1/sqrt(pi) */
-#endif
- }
-#endif
-#endif
-
- /* skip central shifts when summing shift forces */
- if (nb_sci.shift == CENTRAL)
- {
- bCalcFshift = false;
- }
-
- fshift_buf = make_float3(0.0f);
-
- /* loop over the j clusters = seen by any of the atoms in the current super-cluster */
- for (j4 = cij4_start; j4 < cij4_end; j4++)
- {
- wexcl_idx = pl_cj4[j4].imei[widx].excl_ind;
- imask = pl_cj4[j4].imei[widx].imask;
- wexcl = excl[wexcl_idx].pair[(tidx) & (WARP_SIZE - 1)];
-
-#ifndef PRUNE_NBL
- if (imask)
-#endif
- {
- /* nvcc >v4.1 doesn't like this loop, it refuses to unroll it */
-#if CUDA_VERSION >= 4010
- #pragma unroll 4
-#endif
- for (jm = 0; jm < NBNXN_GPU_JGROUP_SIZE; jm++)
- {
- mask_ji = (imask >> (jm * CL_SIZE)) & supercl_interaction_mask;
- if (mask_ji)
- {
- nsubi = __popc(mask_ji);
-
- cj = pl_cj4[j4].cj[jm];
- aj = cj * CL_SIZE + tidxj;
-
- /* load j atom data */
- xqbuf = xq[aj];
- xj = make_float3(xqbuf.x, xqbuf.y, xqbuf.z);
- qj_f = nbparam.epsfac * xqbuf.w;
- typej = atom_types[aj];
-
- fcj_buf = make_float3(0.0f);
-
- /* loop over the i-clusters in sci */
- /* #pragma unroll 8
- -- nvcc doesn't like my code, it refuses to unroll it
- which is a pity because here unrolling could help. */
- for (cii = 0; cii < nsubi; cii++)
- {
- i = __ffs(mask_ji) - 1;
- mask_ji &= ~(1U << i);
-
- ci_offset = i; /* i force buffer offset */
-
- ci = sci * NCL_PER_SUPERCL + i; /* i cluster index */
- ai = ci * CL_SIZE + tidxi; /* i atom index */
-
- /* all threads load an atom from i cluster ci into shmem! */
- xqbuf = xqib[i * CL_SIZE + tidxi];
- xi = make_float3(xqbuf.x, xqbuf.y, xqbuf.z);
-
- /* distance between i and j atoms */
- rv = xi - xj;
- r2 = norm2(rv);
-
-#ifdef PRUNE_NBL
- /* If _none_ of the atoms pairs are in cutoff range,
- the bit corresponding to the current
- cluster-pair in imask gets set to 0. */
- if (!__any(r2 < rlist_sq))
- {
- imask &= ~(1U << (jm * NCL_PER_SUPERCL + i));
- }
-#endif
-
- int_bit = ((wexcl >> (jm * NCL_PER_SUPERCL + i)) & 1) ? 1.0f : 0.0f;
-
- /* cutoff & exclusion check */
-#if defined EL_EWALD_TAB || defined EL_RF
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
-#else
- if (r2 < rcoulomb_sq * int_bit)
-#endif
- {
- /* load the rest of the i-atom parameters */
- qi = xqbuf.w;
- typei = atom_types[ai];
-
- /* LJ 6*C6 and 12*C12 */
- c6 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej));
- c12 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej) + 1);
-
- /* avoid NaN for excluded pairs at r=0 */
- r2 += (1.0f - int_bit) * NBNXN_AVOID_SING_R2_INC;
-
- inv_r = rsqrt(r2);
- inv_r2 = inv_r * inv_r;
- inv_r6 = inv_r2 * inv_r2 * inv_r2;
-#if defined EL_EWALD_TAB || defined EL_RF
- /* We could mask inv_r2, but with Ewald
- * masking both inv_r6 and F_invr is faster */
- inv_r6 *= int_bit;
-#endif
-
- F_invr = inv_r6 * (c12 * inv_r6 - c6) * inv_r2;
-
-#ifdef CALC_ENERGIES
- E_lj_p = int_bit * (c12 * (inv_r6 * inv_r6 - lj_shift * lj_shift) * 0.08333333f - c6 * (inv_r6 - lj_shift) * 0.16666667f);
-#endif
-
-#ifdef VDW_CUTOFF_CHECK
- /* this enables twin-range cut-offs (rvdw < rcoulomb <= rlist) */
- vdw_in_range = (r2 < rvdw_sq) ? 1.0f : 0.0f;
- F_invr *= vdw_in_range;
-#ifdef CALC_ENERGIES
- E_lj_p *= vdw_in_range;
-#endif
-#endif
-#ifdef CALC_ENERGIES
- E_lj += E_lj_p;
-#endif
-
-
-#ifdef EL_CUTOFF
- F_invr += qi * qj_f * inv_r2 * inv_r;
-#endif
-#ifdef EL_RF
- F_invr += qi * qj_f * (int_bit*inv_r2 * inv_r - two_k_rf);
-#endif
-#ifdef EL_EWALD_TAB
- F_invr += qi * qj_f * (int_bit*inv_r2 - interpolate_coulomb_force_r(r2 * inv_r, coulomb_tab_scale)) * inv_r;
-#endif /* EL_EWALD_TAB */
-
-#ifdef CALC_ENERGIES
-#ifdef EL_CUTOFF
- E_el += qi * qj_f * (inv_r - c_rf);
-#endif
-#ifdef EL_RF
- E_el += qi * qj_f * (int_bit*inv_r + 0.5f * two_k_rf * r2 - c_rf);
-#endif
-#ifdef EL_EWALD_TAB
- /* 1.0f - erff is faster than erfcf */
- E_el += qi * qj_f * (inv_r * (int_bit - erff(r2 * inv_r * beta)) - int_bit * ewald_shift);
-#endif
-#endif
- f_ij = rv * F_invr;
-
- /* accumulate j forces in registers */
- fcj_buf -= f_ij;
-
- /* accumulate i forces in registers */
- fci_buf[ci_offset] += f_ij;
- }
- }
-
- /* store j forces in shmem */
- f_buf[ tidx] = fcj_buf.x;
- f_buf[ FBUF_STRIDE + tidx] = fcj_buf.y;
- f_buf[2 * FBUF_STRIDE + tidx] = fcj_buf.z;
-
- /* reduce j forces */
- reduce_force_j_generic(f_buf, f, tidxi, tidxj, aj);
- }
- }
-#ifdef PRUNE_NBL
- /* Update the imask with the new one which does not contain the
- out of range clusters anymore. */
- pl_cj4[j4].imei[widx].imask = imask;
-#endif
- }
- }
-
- /* reduce i forces */
- for(ci_offset = 0; ci_offset < NCL_PER_SUPERCL; ci_offset++)
- {
- ai = (sci * NCL_PER_SUPERCL + ci_offset) * CL_SIZE + tidxi;
- f_buf[ tidx] = fci_buf[ci_offset].x;
- f_buf[ FBUF_STRIDE + tidx] = fci_buf[ci_offset].y;
- f_buf[2 * FBUF_STRIDE + tidx] = fci_buf[ci_offset].z;
- __syncthreads();
- reduce_force_i(f_buf, f,
- &fshift_buf, bCalcFshift,
- tidxi, tidxj, ai);
- __syncthreads();
- }
-
- /* add up local shift forces into global mem */
- if (bCalcFshift && tidxj == 0)
- {
- atomicAdd(&atdat.fshift[nb_sci.shift].x, fshift_buf.x);
- atomicAdd(&atdat.fshift[nb_sci.shift].y, fshift_buf.y);
- atomicAdd(&atdat.fshift[nb_sci.shift].z, fshift_buf.z);
- }
-
-#ifdef CALC_ENERGIES
- /* flush the energies to shmem and reduce them */
- f_buf[ tidx] = E_lj;
- f_buf[FBUF_STRIDE + tidx] = E_el;
- reduce_energy_pow2(f_buf + (tidx & WARP_SIZE), e_lj, e_el, tidx & ~WARP_SIZE);
-#endif
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff