From: Berk Hess Date: Wed, 24 Aug 2016 11:12:21 +0000 (+0200) Subject: Merge branch release-5-1 into release-2016 X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=0986ec764ea5c3515ee9f1ce084ad4fa241754f5;p=alexxy%2Fgromacs.git Merge branch release-5-1 into release-2016 Also applied the merged fix to nbnxn_cuda_kernel_fermi.cuh. Change-Id: I79d0cb59214290097d6f356e35dd13c4eadaed75 --- 0986ec764ea5c3515ee9f1ce084ad4fa241754f5 diff --cc src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh index 0623603903,0000000000..a84f45a54d mode 100644,000000..100644 --- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh +++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh @@@ -1,574 -1,0 +1,574 @@@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by + * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + * and including many others, as listed in the AUTHORS file in the + * top-level source directory and at http://www.gromacs.org. + * + * GROMACS is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * GROMACS is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with GROMACS; if not, see + * http://www.gnu.org/licenses, or write to the Free Software Foundation, + * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + * + * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org. + * + * To help us fund GROMACS development, we humbly ask that you cite + * the research papers on the package. Check out http://www.gromacs.org. + */ + +/*! \internal \file + * \brief + * CUDA non-bonded kernel used through preprocessor-based code generation + * of multiple kernel flavors for CC 2.x, see nbnxn_cuda_kernels.cuh. + * + * NOTE: No include fence as it is meant to be included multiple times. + * + * \author Szilárd Páll + * \author Berk Hess + * \ingroup module_mdlib + */ + +#include "gromacs/gpu_utils/cuda_arch_utils.cuh" +#include "gromacs/math/utilities.h" +#include "gromacs/pbcutil/ishift.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. + */ + +#if GMX_PTX_ARCH >= 300 +#error "nbnxn_cuda_kernel_fermi.cuh included with GMX_PTX_ARCH >= 300" +#endif + +#if defined EL_EWALD_ANA || defined EL_EWALD_TAB +/* Note: convenience macro, needs to be undef-ed at the end of the file. */ +#define EL_EWALD_ANY +#endif + +#if defined EL_EWALD_ANY || defined EL_RF || defined LJ_EWALD || (defined EL_CUTOFF && defined CALC_ENERGIES) +/* Macro to control the calculation of exclusion forces in the kernel + * We do that with Ewald (elec/vdw) and RF. Cut-off only has exclusion + * energy terms. + * + * Note: convenience macro, needs to be undef-ed at the end of the file. + */ +#define EXCLUSION_FORCES +#endif + +#if defined LJ_EWALD_COMB_GEOM || defined LJ_EWALD_COMB_LB +/* Note: convenience macro, needs to be undef-ed at the end of the file. */ +#define LJ_EWALD +#endif + +#if defined LJ_COMB_GEOM || defined LJ_COMB_LB +#define LJ_COMB +#endif + +/* + Kernel launch parameters: + - #blocks = #pair lists, blockId = pair list Id + - #threads = c_clSize^2 + - shmem = see nbnxn_cuda.cu:calc_shmem_required() + + Each thread calculates an i force-component taking one pair of i-j atoms. + */ + +/**@{*/ +/*! \brief Definition of kernel launch configuration parameters for CC 2.x. + */ + +/* Kernel launch bounds, 16 blocks/multiprocessor can be kept in flight. */ +#define THREADS_PER_BLOCK (c_clSize*c_clSize) + +__launch_bounds__(THREADS_PER_BLOCK) +#ifdef PRUNE_NBL +#ifdef CALC_ENERGIES +__global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _VF_prune_cuda) +#else +__global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _F_prune_cuda) +#endif /* CALC_ENERGIES */ +#else +#ifdef CALC_ENERGIES +__global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _VF_cuda) +#else +__global__ void NB_KERNEL_FUNC_NAME(nbnxn_kernel, _F_cuda) +#endif /* CALC_ENERGIES */ +#endif /* PRUNE_NBL */ +(const cu_atomdata_t atdat, + const cu_nbparam_t nbparam, + const cu_plist_t plist, + bool bCalcFshift) +#ifdef FUNCTION_DECLARATION_ONLY +; /* Only do function declaration, omit the function body. */ +#else +{ + /* 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; +#ifndef LJ_COMB + const int *atom_types = atdat.atom_types; + int ntypes = atdat.ntypes; +#else + const float2 *lj_comb = atdat.lj_comb; + float2 ljcp_i, ljcp_j; +#endif + 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 LJ_EWALD + float lje_coeff2, lje_coeff6_6; +#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 EL_EWALD_ANA + float beta2 = nbparam.ewald_beta*nbparam.ewald_beta; + float beta3 = nbparam.ewald_beta*nbparam.ewald_beta*nbparam.ewald_beta; +#endif +#ifdef PRUNE_NBL + float rlist_sq = nbparam.rlist_sq; +#endif + +#ifdef CALC_ENERGIES +#ifdef EL_EWALD_ANY + float beta = nbparam.ewald_beta; + float ewald_shift = nbparam.sh_ewald; +#else + float c_rf = nbparam.c_rf; +#endif /* EL_EWALD_ANY */ + float *e_lj = atdat.e_lj; + float *e_el = atdat.e_el; +#endif /* CALC_ENERGIES */ + + /* 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, + ai, aj, + cij4_start, cij4_end; +#ifndef LJ_COMB + int typei, typej; +#endif + int i, jm, j4, wexcl_idx; + float qi, qj_f, + r2, inv_r, inv_r2; +#if !defined LJ_COMB_LB || defined CALC_ENERGIES + float inv_r6, c6, c12; +#endif +#ifdef LJ_COMB_LB + float sigma, epsilon; +#endif + float int_bit, + F_invr; +#ifdef CALC_ENERGIES + float E_lj, E_el; +#endif +#if defined CALC_ENERGIES || defined LJ_POT_SWITCH + float E_lj_p; +#endif + unsigned int wexcl, imask, mask_ji; + float4 xqbuf; + float3 xi, xj, rv, f_ij, fcj_buf; + float3 fci_buf[c_numClPerSupercl]; /* i force buffer */ + nbnxn_sci_t nb_sci; + + /*! i-cluster interaction mask for a super-cluster with all c_numClPerSupercl=8 bits set */ + const unsigned superClInteractionMask = ((1U << c_numClPerSupercl) - 1U); + + /* shmem buffer for i x+q pre-loading */ + extern __shared__ float4 xqib[]; + + /* shmem buffer for cj, for each warp separately */ + int *cjs = ((int *)(xqib + c_numClPerSupercl * c_clSize)); + /* shmem j force buffer */ + float *f_buf = (float *)(cjs + c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize); + + 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 */ + + { + /* Pre-load i-atom x and q into shared memory */ + ci = sci * c_numClPerSupercl + tidxj; + ai = ci * c_clSize + tidxi; + + xqbuf = xq[ai] + shift_vec[nb_sci.shift]; + xqbuf.w *= nbparam.epsfac; + xqib[tidxj * c_clSize + tidxi] = xqbuf; + } + __syncthreads(); + + for (i = 0; i < c_numClPerSupercl; i++) + { + fci_buf[i] = make_float3(0.0f); + } + +#ifdef LJ_EWALD + /* TODO: we are trading registers with flops by keeping lje_coeff-s, try re-calculating it later */ + lje_coeff2 = nbparam.ewaldcoeff_lj*nbparam.ewaldcoeff_lj; + lje_coeff6_6 = lje_coeff2*lje_coeff2*lje_coeff2*c_oneSixth; +#endif + + +#ifdef CALC_ENERGIES + E_lj = 0.0f; + E_el = 0.0f; + +#ifdef EXCLUSION_FORCES /* Ewald or RF */ + if (nb_sci.shift == CENTRAL && pl_cj4[cij4_start].cj[0] == sci*c_numClPerSupercl) + { + /* we have the diagonal: add the charge and LJ self interaction energy term */ + for (i = 0; i < c_numClPerSupercl; i++) + { +#if defined EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF + qi = xqib[i * c_clSize + tidxi].w; + E_el += qi*qi; +#endif + +#ifdef LJ_EWALD + E_lj += tex1Dfetch(nbfp_texref, atom_types[(sci*c_numClPerSupercl + i)*c_clSize + tidxi]*(ntypes + 1)*2); +#endif + } + + /* divide the self term(s) equally over the j-threads, then multiply with the coefficients. */ +#ifdef LJ_EWALD + E_lj /= c_clSize; + E_lj *= 0.5f*c_oneSixth*lje_coeff6_6; +#endif + +#if defined EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF + /* Correct for epsfac^2 due to adding qi^2 */ + E_el /= nbparam.epsfac*c_clSize; +#if defined EL_RF || defined EL_CUTOFF + E_el *= -0.5f*c_rf; +#else + E_el *= -beta*M_FLOAT_1_SQRTPI; /* last factor 1/sqrt(pi) */ +#endif +#endif /* EL_EWALD_ANY || defined EL_RF || defined EL_CUTOFF */ + } +#endif /* EXCLUSION_FORCES */ + +#endif /* CALC_ENERGIES */ + + /* 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 + { + /* Pre-load cj into shared memory on both warps separately */ + if ((tidxj == 0 || tidxj == 4) && tidxi < c_nbnxnGpuJgroupSize) + { + cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize/c_splitClSize] = pl_cj4[j4].cj[tidxi]; + } + + /* Unrolling this loop with pruning leads to register spilling; + Tested with up to nvcc 7.5 */ +#if !defined PRUNE_NBL +#pragma unroll 4 +#endif + for (jm = 0; jm < c_nbnxnGpuJgroupSize; jm++) + { + if (imask & (superClInteractionMask << (jm * c_numClPerSupercl))) + { + mask_ji = (1U << (jm * c_numClPerSupercl)); + + cj = cjs[jm + (tidxj & 4) * c_nbnxnGpuJgroupSize/c_splitClSize]; + aj = cj * c_clSize + tidxj; + + /* load j atom data */ + xqbuf = xq[aj]; + xj = make_float3(xqbuf.x, xqbuf.y, xqbuf.z); + qj_f = xqbuf.w; +#ifndef LJ_COMB + typej = atom_types[aj]; +#else + ljcp_j = lj_comb[aj]; +#endif + + fcj_buf = make_float3(0.0f); + +#if !defined PRUNE_NBL +#pragma unroll 8 +#endif + for (i = 0; i < c_numClPerSupercl; i++) + { + if (imask & mask_ji) + { + ci = sci * c_numClPerSupercl + i; /* i cluster index */ + ai = ci * c_clSize + tidxi; /* i atom index */ + + /* all threads load an atom from i cluster ci into shmem! */ + xqbuf = xqib[i * c_clSize + 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 &= ~mask_ji; + } +#endif + + int_bit = (wexcl & mask_ji) ? 1.0f : 0.0f; + + /* cutoff & exclusion check */ +#ifdef EXCLUSION_FORCES + 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; + +#ifndef LJ_COMB + /* LJ 6*C6 and 12*C12 */ + typei = atom_types[ai]; + c6 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej)); + c12 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej) + 1); +#else + ljcp_i = lj_comb[ai]; +#ifdef LJ_COMB_GEOM + c6 = ljcp_i.x * ljcp_j.x; + c12 = ljcp_i.y * ljcp_j.y; +#else + /* LJ 2^(1/6)*sigma and 12*epsilon */ + sigma = ljcp_i.x + ljcp_j.x; + epsilon = ljcp_i.y * ljcp_j.y; +#if defined CALC_ENERGIES || defined LJ_FORCE_SWITCH || defined LJ_POT_SWITCH + convert_sigma_epsilon_to_c6_c12(sigma, epsilon, &c6, &c12); +#endif +#endif /* LJ_COMB_GEOM */ +#endif /* LJ_COMB */ + + // Ensure distance do not become so small that r^-12 overflows + r2 = max(r2, NBNXN_MIN_RSQ); + + inv_r = rsqrt(r2); + inv_r2 = inv_r * inv_r; +#if !defined LJ_COMB_LB || defined CALC_ENERGIES + inv_r6 = inv_r2 * inv_r2 * inv_r2; +#ifdef EXCLUSION_FORCES + /* We could mask inv_r2, but with Ewald + * masking both inv_r6 and F_invr is faster */ + inv_r6 *= int_bit; +#endif /* EXCLUSION_FORCES */ + + F_invr = inv_r6 * (c12 * inv_r6 - c6) * inv_r2; +#if defined CALC_ENERGIES || defined LJ_POT_SWITCH + E_lj_p = int_bit * (c12 * (inv_r6 * inv_r6 + nbparam.repulsion_shift.cpot)*c_oneTwelveth - + c6 * (inv_r6 + nbparam.dispersion_shift.cpot)*c_oneSixth); +#endif +#else /* !LJ_COMB_LB || CALC_ENERGIES */ + float sig_r = sigma*inv_r; + float sig_r2 = sig_r*sig_r; + float sig_r6 = sig_r2*sig_r2*sig_r2; +#ifdef EXCLUSION_FORCES + sig_r6 *= int_bit; +#endif /* EXCLUSION_FORCES */ + + F_invr = epsilon * sig_r6 * (sig_r6 - 1.0f) * inv_r2; +#endif /* !LJ_COMB_LB || CALC_ENERGIES */ + +#ifdef LJ_FORCE_SWITCH +#ifdef CALC_ENERGIES + calculate_force_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p); +#else + calculate_force_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr); +#endif /* CALC_ENERGIES */ +#endif /* LJ_FORCE_SWITCH */ + + +#ifdef LJ_EWALD +#ifdef LJ_EWALD_COMB_GEOM +#ifdef CALC_ENERGIES + calculate_lj_ewald_comb_geom_F_E(nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, int_bit, &F_invr, &E_lj_p); +#else + calculate_lj_ewald_comb_geom_F(nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, &F_invr); +#endif /* CALC_ENERGIES */ +#elif defined LJ_EWALD_COMB_LB + calculate_lj_ewald_comb_LB_F_E(nbparam, typei, typej, r2, inv_r2, lje_coeff2, lje_coeff6_6, +#ifdef CALC_ENERGIES + int_bit, &F_invr, &E_lj_p +#else + 0, &F_invr, NULL +#endif /* CALC_ENERGIES */ + ); +#endif /* LJ_EWALD_COMB_GEOM */ +#endif /* LJ_EWALD */ + ++#ifdef LJ_POT_SWITCH ++#ifdef CALC_ENERGIES ++ calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p); ++#else ++ calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p); ++#endif /* CALC_ENERGIES */ ++#endif /* LJ_POT_SWITCH */ ++ +#ifdef VDW_CUTOFF_CHECK + /* Separate VDW cut-off check to enable 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 /* VDW_CUTOFF_CHECK */ + - #ifdef LJ_POT_SWITCH - #ifdef CALC_ENERGIES - calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p); - #else - calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p); - #endif /* CALC_ENERGIES */ - #endif /* LJ_POT_SWITCH */ - +#ifdef CALC_ENERGIES + E_lj += E_lj_p; +#endif + + +#ifdef EL_CUTOFF +#ifdef EXCLUSION_FORCES + F_invr += qi * qj_f * int_bit * inv_r2 * inv_r; +#else + F_invr += qi * qj_f * inv_r2 * inv_r; +#endif +#endif +#ifdef EL_RF + F_invr += qi * qj_f * (int_bit*inv_r2 * inv_r - two_k_rf); +#endif +#if defined EL_EWALD_ANA + F_invr += qi * qj_f * (int_bit*inv_r2*inv_r + pmecorrF(beta2*r2)*beta3); +#elif defined 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_ANA/TAB */ + +#ifdef CALC_ENERGIES +#ifdef EL_CUTOFF + E_el += qi * qj_f * (int_bit*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_ANY + /* 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 /* EL_EWALD_ANY */ +#endif + f_ij = rv * F_invr; + + /* accumulate j forces in registers */ + fcj_buf -= f_ij; + + /* accumulate i forces in registers */ + fci_buf[i] += f_ij; + } + } + + /* shift the mask bit by 1 */ + mask_ji += mask_ji; + } + + /* reduce j forces */ + /* store j forces in shmem */ + f_buf[ tidx] = fcj_buf.x; + f_buf[ c_fbufStride + tidx] = fcj_buf.y; + f_buf[2 * c_fbufStride + tidx] = fcj_buf.z; + + 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 + } + } + + /* skip central shifts when summing shift forces */ + if (nb_sci.shift == CENTRAL) + { + bCalcFshift = false; + } + + float fshift_buf = 0.0f; + + /* reduce i forces */ + for (i = 0; i < c_numClPerSupercl; i++) + { + ai = (sci * c_numClPerSupercl + i) * c_clSize + tidxi; + f_buf[ tidx] = fci_buf[i].x; + f_buf[ c_fbufStride + tidx] = fci_buf[i].y; + f_buf[2 * c_fbufStride + tidx] = fci_buf[i].z; + __syncthreads(); + reduce_force_i(f_buf, f, + &fshift_buf, bCalcFshift, + tidxi, tidxj, ai); + __syncthreads(); + } + + /* add up local shift forces into global mem, tidxj indexes x,y,z */ + if (bCalcFshift && tidxj < 3) + { + atomicAdd(&(atdat.fshift[nb_sci.shift].x) + tidxj, fshift_buf); + } + +#ifdef CALC_ENERGIES + /* flush the energies to shmem and reduce them */ + f_buf[ tidx] = E_lj; + f_buf[c_fbufStride + tidx] = E_el; + reduce_energy_pow2(f_buf + (tidx & warp_size), e_lj, e_el, tidx & ~warp_size); +#endif +} +#endif /* FUNCTION_DECLARATION_ONLY */ + +#undef THREADS_PER_BLOCK + +#undef EL_EWALD_ANY +#undef EXCLUSION_FORCES +#undef LJ_EWALD + +#undef LJ_COMB