291 lines
13 KiB
Plaintext
291 lines
13 KiB
Plaintext
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extern "C" {
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#include <stdio.h>
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//---
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#include <cuda.h>
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#include <driver_types.h>
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//---
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#include <likwid-marker.h>
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//---
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#include <atom.h>
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#include <device.h>
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#include <neighbor.h>
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#include <parameter.h>
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#include <stats.h>
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#include <timing.h>
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#include <util.h>
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}
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extern "C" {
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extern MD_FLOAT *cuda_cl_x;
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extern MD_FLOAT *cuda_cl_v;
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extern MD_FLOAT *cuda_cl_f;
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extern int *cuda_neighbors;
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extern int *cuda_numneigh;
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extern int *cuda_natoms;
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extern int *natoms;
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extern int *ngatoms;
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extern int *cuda_border_map;
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extern int *cuda_jclusters_natoms;
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extern MD_FLOAT *cuda_bbminx, *cuda_bbmaxx;
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extern MD_FLOAT *cuda_bbminy, *cuda_bbmaxy;
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extern MD_FLOAT *cuda_bbminz, *cuda_bbmaxz;
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extern int *cuda_PBCx, *cuda_PBCy, *cuda_PBCz;
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extern int isReneighboured;
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extern int *cuda_iclusters;
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extern int *cuda_nclusters;
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extern MD_FLOAT *cuda_scl_x;
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extern MD_FLOAT *cuda_scl_v;
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extern MD_FLOAT *cuda_scl_f;
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}
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#ifdef USE_SUPER_CLUSTERS
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extern "C"
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void alignDataToSuperclusters(Atom *atom) {
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for (int sci = 0; sci < atom->Nsclusters_local; sci++) {
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const unsigned int scl_offset = sci * SCLUSTER_SIZE * 3 * CLUSTER_M;
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for (int ci = 0, scci = scl_offset; ci < atom->siclusters[sci].nclusters; ci++, scci += CLUSTER_M) {
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MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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MD_FLOAT *ci_v = &atom->cl_v[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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MD_FLOAT *ci_f = &atom->cl_f[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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/*
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MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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MD_FLOAT *ci_v = &atom->cl_v[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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MD_FLOAT *ci_f = &atom->cl_f[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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*/
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memcpy(&atom->scl_x[scci], &ci_x[0], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_x[scci + SCLUSTER_SIZE * CLUSTER_M], &ci_x[0 + CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_x[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], &ci_x[0 + 2 * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_v[scci], &ci_v[0], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_v[scci + SCLUSTER_SIZE * CLUSTER_M], &ci_v[0 + CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_v[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], &ci_v[0 + 2 * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_f[scci], &ci_f[0], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_f[scci + SCLUSTER_SIZE * CLUSTER_M], &ci_f[0 + CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&atom->scl_f[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], &ci_f[0 + 2 * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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}
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}
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}
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extern "C"
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void alignDataFromSuperclusters(Atom *atom) {
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for (int sci = 0; sci < atom->Nsclusters_local; sci++) {
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const unsigned int scl_offset = sci * SCLUSTER_SIZE * 3 * CLUSTER_M;
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for (int ci = 0, scci = scl_offset; ci < atom->siclusters[sci].nclusters; ci++, scci += CLUSTER_M) {
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MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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MD_FLOAT *ci_v = &atom->cl_v[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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MD_FLOAT *ci_f = &atom->cl_f[CI_VECTOR_BASE_INDEX(atom->icluster_idx[SCLUSTER_SIZE * sci + ci])];
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/*
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MD_FLOAT *ci_x = &atom->cl_x[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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MD_FLOAT *ci_v = &atom->cl_v[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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MD_FLOAT *ci_f = &atom->cl_f[CI_VECTOR_BASE_INDEX(atom->siclusters[sci].iclusters[ci])];
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*/
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memcpy(&ci_x[0], &atom->scl_x[scci], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_x[0 + CLUSTER_M], &atom->scl_x[scci + SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_x[0 + 2 * CLUSTER_M], &atom->scl_x[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_v[0], &atom->scl_v[scci], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_v[0 + CLUSTER_M], &atom->scl_v[scci + SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_v[0 + 2 * CLUSTER_M], &atom->scl_v[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_f[0], &atom->scl_f[scci], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_f[0 + CLUSTER_M], &atom->scl_f[scci + SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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memcpy(&ci_f[0 + 2 * CLUSTER_M], &atom->scl_f[scci + 2 * SCLUSTER_SIZE * CLUSTER_M], CLUSTER_M * sizeof(MD_FLOAT));
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}
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}
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}
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__global__ void cudaInitialIntegrateSup_warp(MD_FLOAT *cuda_cl_x, MD_FLOAT *cuda_cl_v, MD_FLOAT *cuda_cl_f,
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int *cuda_nclusters,
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int *cuda_natoms,
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int Nsclusters_local, MD_FLOAT dtforce, MD_FLOAT dt) {
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unsigned int sci_pos = blockDim.x * blockIdx.x + threadIdx.x;
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//unsigned int cii_pos = blockDim.y * blockIdx.y + threadIdx.y;
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if (sci_pos >= Nsclusters_local) return;
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//unsigned int ci_pos = cii_pos / CLUSTER_M;
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//unsigned int scii_pos = cii_pos % CLUSTER_M;
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//if (ci_pos >= cuda_nclusters[sci_pos]) return;
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//if (scii_pos >= cuda_natoms[ci_pos]) return;
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int ci_vec_base = SCI_VECTOR_BASE_INDEX(sci_pos);
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MD_FLOAT *ci_x = &cuda_cl_x[ci_vec_base];
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MD_FLOAT *ci_v = &cuda_cl_v[ci_vec_base];
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MD_FLOAT *ci_f = &cuda_cl_f[ci_vec_base];
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for (int scii_pos = 0; scii_pos < SCLUSTER_M; scii_pos++) {
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ci_v[SCL_X_OFFSET + scii_pos] += dtforce * ci_f[SCL_X_OFFSET + scii_pos];
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ci_v[SCL_Y_OFFSET + scii_pos] += dtforce * ci_f[SCL_Y_OFFSET + scii_pos];
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ci_v[SCL_Z_OFFSET + scii_pos] += dtforce * ci_f[SCL_Z_OFFSET + scii_pos];
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ci_x[SCL_X_OFFSET + scii_pos] += dt * ci_v[SCL_X_OFFSET + scii_pos];
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ci_x[SCL_Y_OFFSET + scii_pos] += dt * ci_v[SCL_Y_OFFSET + scii_pos];
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ci_x[SCL_Z_OFFSET + scii_pos] += dt * ci_v[SCL_Z_OFFSET + scii_pos];
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}
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}
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__global__ void cudaFinalIntegrateSup_warp(MD_FLOAT *cuda_cl_v, MD_FLOAT *cuda_cl_f,
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int *cuda_nclusters, int *cuda_natoms,
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int Nsclusters_local, MD_FLOAT dtforce) {
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unsigned int sci_pos = blockDim.x * blockIdx.x + threadIdx.x;
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//unsigned int cii_pos = blockDim.y * blockIdx.y + threadIdx.y;
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if (sci_pos >= Nsclusters_local) return;
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//unsigned int ci_pos = cii_pos / CLUSTER_M;
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//unsigned int scii_pos = cii_pos % CLUSTER_M;
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//if (ci_pos >= cuda_nclusters[sci_pos]) return;
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//if (scii_pos >= cuda_natoms[ci_pos]) return;
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int ci_vec_base = SCI_VECTOR_BASE_INDEX(sci_pos);
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MD_FLOAT *ci_v = &cuda_cl_v[ci_vec_base];
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MD_FLOAT *ci_f = &cuda_cl_f[ci_vec_base];
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for (int scii_pos = 0; scii_pos < SCLUSTER_M; scii_pos++) {
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ci_v[SCL_X_OFFSET + scii_pos] += dtforce * ci_f[SCL_X_OFFSET + scii_pos];
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ci_v[SCL_Y_OFFSET + scii_pos] += dtforce * ci_f[SCL_Y_OFFSET + scii_pos];
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ci_v[SCL_Z_OFFSET + scii_pos] += dtforce * ci_f[SCL_Z_OFFSET + scii_pos];
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}
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}
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__global__ void computeForceLJSup_cuda_warp(MD_FLOAT *cuda_cl_x, MD_FLOAT *cuda_cl_f,
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int *cuda_nclusters, int *cuda_iclusters,
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int Nsclusters_local,
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int *cuda_numneigh, int *cuda_neighs, int half_neigh, int maxneighs,
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MD_FLOAT cutforcesq, MD_FLOAT sigma6, MD_FLOAT epsilon) {
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unsigned int sci_pos = blockDim.x * blockIdx.x + threadIdx.x;
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unsigned int scii_pos = blockDim.y * blockIdx.y + threadIdx.y;
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unsigned int cjj_pos = blockDim.z * blockIdx.z + threadIdx.z;
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if ((sci_pos >= Nsclusters_local) || (scii_pos >= SCLUSTER_M) || (cjj_pos >= CLUSTER_N)) return;
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unsigned int ci_pos = scii_pos / CLUSTER_M;
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unsigned int cii_pos = scii_pos % CLUSTER_M;
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if (ci_pos >= cuda_nclusters[sci_pos]) return;
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int ci_cj0 = CJ0_FROM_CI(ci_pos);
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int ci_vec_base = SCI_VECTOR_BASE_INDEX(sci_pos);
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MD_FLOAT *ci_x = &cuda_cl_x[ci_vec_base];
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MD_FLOAT *ci_f = &cuda_cl_f[ci_vec_base];
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//int numneighs = cuda_numneigh[ci_pos];
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int numneighs = cuda_numneigh[cuda_iclusters[SCLUSTER_SIZE * sci_pos + ci_pos]];
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for(int k = 0; k < numneighs; k++) {
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int cj = (&cuda_neighs[cuda_iclusters[SCLUSTER_SIZE * sci_pos + ci_pos] * maxneighs])[k];
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// TODO Make cj accessible from super cluster data alignment (not reachable right now)
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int cj_vec_base = SCJ_VECTOR_BASE_INDEX(cj);
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MD_FLOAT *cj_x = &cuda_cl_x[cj_vec_base];
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MD_FLOAT *cj_f = &cuda_cl_f[cj_vec_base];
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MD_FLOAT xtmp = ci_x[SCL_CL_X_OFFSET(ci_pos) + cii_pos];
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MD_FLOAT ytmp = ci_x[SCL_CL_Y_OFFSET(ci_pos) + cii_pos];
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MD_FLOAT ztmp = ci_x[SCL_CL_Z_OFFSET(ci_pos) + cii_pos];
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MD_FLOAT fix = 0;
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MD_FLOAT fiy = 0;
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MD_FLOAT fiz = 0;
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int cond;
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#if CLUSTER_M == CLUSTER_N
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cond = half_neigh ? (ci_cj0 != cj || cii_pos < cjj_pos) :
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(ci_cj0 != cj || cii_pos != cjj_pos);
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#elif CLUSTER_M < CLUSTER_N
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cond = half_neigh ? (ci_cj0 != cj || cii_pos + CLUSTER_M * (ci_pos & 0x1) < cjj_pos) :
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(ci_cj0 != cj || cii_pos + CLUSTER_M * (ci_pos & 0x1) != cjj_pos);
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#endif
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if(cond) {
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MD_FLOAT delx = xtmp - cj_x[SCL_CL_X_OFFSET(ci_pos) + cjj_pos];
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MD_FLOAT dely = ytmp - cj_x[SCL_CL_Y_OFFSET(ci_pos) + cjj_pos];
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MD_FLOAT delz = ztmp - cj_x[SCL_CL_Z_OFFSET(ci_pos) + cjj_pos];
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MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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if(rsq < cutforcesq) {
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MD_FLOAT sr2 = 1.0 / rsq;
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MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
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MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
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if(half_neigh) {
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atomicAdd(&cj_f[SCL_CL_X_OFFSET(ci_pos) + cjj_pos], -delx * force);
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atomicAdd(&cj_f[SCL_CL_Y_OFFSET(ci_pos) + cjj_pos], -dely * force);
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atomicAdd(&cj_f[SCL_CL_Z_OFFSET(ci_pos) + cjj_pos], -delz * force);
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}
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fix += delx * force;
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fiy += dely * force;
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fiz += delz * force;
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atomicAdd(&ci_f[SCL_CL_X_OFFSET(ci_pos) + cii_pos], fix);
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atomicAdd(&ci_f[SCL_CL_Y_OFFSET(ci_pos) + cii_pos], fiy);
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atomicAdd(&ci_f[SCL_CL_Z_OFFSET(ci_pos) + cii_pos], fiz);
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}
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}
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}
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}
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extern "C"
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double computeForceLJSup_cuda(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *stats) {
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DEBUG_MESSAGE("computeForceLJSup_cuda start\r\n");
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MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
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MD_FLOAT sigma6 = param->sigma6;
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MD_FLOAT epsilon = param->epsilon;
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memsetGPU(cuda_cl_f, 0, atom->Nclusters_max * CLUSTER_M * 3 * sizeof(MD_FLOAT));
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if (isReneighboured) {
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for(int ci = 0; ci < atom->Nclusters_local; ci++) {
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memcpyToGPU(&cuda_numneigh[ci], &neighbor->numneigh[ci], sizeof(int));
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memcpyToGPU(&cuda_neighbors[ci * neighbor->maxneighs], &neighbor->neighbors[ci * neighbor->maxneighs], neighbor->numneigh[ci] * sizeof(int));
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}
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for(int sci = 0; sci < atom->Nsclusters_local; sci++) {
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memcpyToGPU(&cuda_nclusters[sci], &atom->siclusters[sci].nclusters, sizeof(int));
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//memcpyToGPU(&cuda_iclusters[sci * SCLUSTER_SIZE], &atom->siclusters[sci].iclusters, sizeof(int) * atom->siclusters[sci].nclusters);
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}
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memcpyToGPU(cuda_iclusters, atom->icluster_idx, atom->Nsclusters_max * SCLUSTER_SIZE * sizeof(int));
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isReneighboured = 0;
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}
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const int threads_num = 1;
|
||
|
|
dim3 block_size = dim3(threads_num, SCLUSTER_M, CLUSTER_N);
|
||
|
|
dim3 grid_size = dim3(atom->Nsclusters_local/threads_num+1, 1, 1);
|
||
|
|
double S = getTimeStamp();
|
||
|
|
LIKWID_MARKER_START("force");
|
||
|
|
computeForceLJSup_cuda_warp<<<grid_size, block_size>>>(cuda_scl_x, cuda_scl_f,
|
||
|
|
cuda_nclusters, cuda_iclusters,
|
||
|
|
atom->Nsclusters_local,
|
||
|
|
cuda_numneigh, cuda_neighbors,
|
||
|
|
neighbor->half_neigh, neighbor->maxneighs, cutforcesq,
|
||
|
|
sigma6, epsilon);
|
||
|
|
cuda_assert("computeForceLJ_cuda", cudaPeekAtLastError());
|
||
|
|
cuda_assert("computeForceLJ_cuda", cudaDeviceSynchronize());
|
||
|
|
LIKWID_MARKER_STOP("force");
|
||
|
|
double E = getTimeStamp();
|
||
|
|
DEBUG_MESSAGE("computeForceLJSup_cuda stop\r\n");
|
||
|
|
return E-S;
|
||
|
|
}
|
||
|
|
#endif //USE_SUPER_CLUSTERS
|