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First changes in the supercluster code

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2023-05-25 01:10:37 +02:00
parent 055a009dbd
commit 924914e4f0
2 changed files with 16 additions and 52 deletions
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4
gromacs/main.c
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@ -288,7 +288,6 @@ int main(int argc, char** argv) {
#endif //defined(CUDA_TARGET) && defined(USE_SUPER_CLUSTERS) #endif //defined(CUDA_TARGET) && defined(USE_SUPER_CLUSTERS)
} }
copyDataFromCUDADevice(&atom); copyDataFromCUDADevice(&atom);
updatePbc(&atom, &param, 0); updatePbc(&atom, &param, 0);
copyDataToCUDADevice(&atom); copyDataToCUDADevice(&atom);
@ -334,9 +333,6 @@ int main(int argc, char** argv) {
finalIntegrate(&param, &atom); finalIntegrate(&param, &atom);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) { if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
computeThermo(n + 1, &param, &atom); computeThermo(n + 1, &param, &atom);
} }

58
gromacs/neighbor.c
View File

@ -192,7 +192,6 @@ int atomDistanceInRange(Atom *atom, int ci, int cj, MD_FLOAT rsq) {
int atomDistanceInRangeGPU(Atom *atom, int sci, int cj, MD_FLOAT rsq) { int atomDistanceInRangeGPU(Atom *atom, int sci, int cj, MD_FLOAT rsq) {
for (int ci = 0; ci < atom->siclusters[sci].nclusters; ci++) { for (int ci = 0; ci < atom->siclusters[sci].nclusters; ci++) {
const int icluster_idx = atom->icluster_idx[SCLUSTER_SIZE * sci + ci]; const int icluster_idx = atom->icluster_idx[SCLUSTER_SIZE * sci + ci];
int ci_vec_base = CI_VECTOR_BASE_INDEX(icluster_idx); int ci_vec_base = CI_VECTOR_BASE_INDEX(icluster_idx);
int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj); int cj_vec_base = CJ_VECTOR_BASE_INDEX(cj);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base]; MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
@ -520,15 +519,6 @@ void buildNeighborGPU(Atom *atom, Neighbor *neighbor) {
new_maxneighs = n; new_maxneighs = n;
} }
} }
for (int scii = 0; scii < atom->siclusters[sci].nclusters; scii++) {
//for(int ci = 0; ci < atom->Nclusters_local; ci++) {
//const int ci = atom->siclusters[sci].iclusters[scii];
}
} }
if(resize) { if(resize) {
@ -907,6 +897,7 @@ void buildClusters(Atom *atom) {
void buildClustersGPU(Atom *atom) { void buildClustersGPU(Atom *atom) {
DEBUG_MESSAGE("buildClustersGPU start\n"); DEBUG_MESSAGE("buildClustersGPU start\n");
atom->Nclusters_local = 0; atom->Nclusters_local = 0;
atom->Nsclusters_local = 0;
/* bin local atoms */ /* bin local atoms */
binAtoms(atom); binAtoms(atom);
@ -917,59 +908,33 @@ void buildClustersGPU(Atom *atom) {
int ac = 0; int ac = 0;
int nclusters = ((c + CLUSTER_M - 1) / CLUSTER_M); int nclusters = ((c + CLUSTER_M - 1) / CLUSTER_M);
if(CLUSTER_N > CLUSTER_M && nclusters % 2) { nclusters++; } if(CLUSTER_N > CLUSTER_M && nclusters % 2) { nclusters++; }
const int supercluster_size = SCLUSTER_SIZE_X * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_Z;
int nsclusters = ((nclusters + supercluster_size - 1) / supercluster_size);
int n_super_clusters_xy = nclusters / (SCLUSTER_SIZE_X * SCLUSTER_SIZE_Y); for(int scl = 0; scl < nsclusters; scl++) {
if (nclusters % (SCLUSTER_SIZE_X * SCLUSTER_SIZE_Y)) n_super_clusters_xy++;
int n_super_clusters = n_super_clusters_xy / SCLUSTER_SIZE_Z;
if (n_super_clusters_xy % SCLUSTER_SIZE_Z) n_super_clusters++;
int cl_count = 0;
for (int scl = 0; scl < n_super_clusters; scl++) {
const int sci = atom->Nsclusters_local; const int sci = atom->Nsclusters_local;
if(sci >= atom->Nsclusters_max) { if(sci >= atom->Nsclusters_max) {
growSuperClusters(atom); growSuperClusters(atom);
} }
if (cl_count >= nclusters) break;
int scl_offset = scl * SCLUSTER_SIZE * CLUSTER_M; int scl_offset = scl * SCLUSTER_SIZE * CLUSTER_M;
MD_FLOAT sc_bbminx = INFINITY, sc_bbmaxx = -INFINITY; MD_FLOAT sc_bbminx = INFINITY, sc_bbmaxx = -INFINITY;
MD_FLOAT sc_bbminy = INFINITY, sc_bbmaxy = -INFINITY; MD_FLOAT sc_bbminy = INFINITY, sc_bbmaxy = -INFINITY;
MD_FLOAT sc_bbminz = INFINITY, sc_bbmaxz = -INFINITY; MD_FLOAT sc_bbminz = INFINITY, sc_bbmaxz = -INFINITY;
atom->siclusters[sci].nclusters = 0;
for(int scl_z = 0; scl_z < SCLUSTER_SIZE_Z; scl_z++) { for(int scl_z = 0; scl_z < SCLUSTER_SIZE_Z; scl_z++) {
if (cl_count >= nclusters) break;
const int atom_scl_z_offset = scl_offset + scl_z * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M; const int atom_scl_z_offset = scl_offset + scl_z * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M;
const int atom_scl_z_end_idx = MIN(atom_scl_z_offset + SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M - 1, c - 1);
const int atom_scl_z_end_idx = MIN(atom_scl_z_offset +
SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M - 1, c - 1);
sortAtomsByCoord(atom, YY, bin, atom_scl_z_offset, atom_scl_z_end_idx); sortAtomsByCoord(atom, YY, bin, atom_scl_z_offset, atom_scl_z_end_idx);
for(int scl_y = 0; scl_y < SCLUSTER_SIZE_Y; scl_y++) { for(int scl_y = 0; scl_y < SCLUSTER_SIZE_Y; scl_y++) {
const int atom_scl_y_offset = scl_offset + scl_z * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M + scl_y * SCLUSTER_SIZE_Y * CLUSTER_M;
if (cl_count >= nclusters) break; const int atom_scl_y_end_idx = MIN(atom_scl_y_offset + SCLUSTER_SIZE_X * CLUSTER_M - 1, c - 1);
const int atom_scl_y_offset = scl_offset +
scl_z * SCLUSTER_SIZE_Y * SCLUSTER_SIZE_X * CLUSTER_M +
scl_y * SCLUSTER_SIZE_Y * CLUSTER_M;
const int atom_scl_y_end_idx = MIN(atom_scl_y_offset +
SCLUSTER_SIZE_X * CLUSTER_M - 1, c - 1);
sortAtomsByCoord(atom, XX, bin, atom_scl_y_offset, atom_scl_y_end_idx); sortAtomsByCoord(atom, XX, bin, atom_scl_y_offset, atom_scl_y_end_idx);
for(int scl_x = 0; scl_x < SCLUSTER_SIZE_X; scl_x++) { for(int scl_x = 0; scl_x < SCLUSTER_SIZE_X; scl_x++) {
if (cl_count >= nclusters) break; const int cluster_sup_idx = scl_z * SCLUSTER_SIZE_Z * SCLUSTER_SIZE_Y + scl_y * SCLUSTER_SIZE_X + scl_x;
cl_count++;
const int cluster_sup_idx = scl_z * SCLUSTER_SIZE_Z * SCLUSTER_SIZE_Y +
scl_y * SCLUSTER_SIZE_X + scl_x;
const int ci = atom->Nclusters_local; const int ci = atom->Nclusters_local;
if(ci >= atom->Nclusters_max) { if(ci >= atom->Nclusters_max) {
growClusters(atom); growClusters(atom);
@ -1008,7 +973,6 @@ void buildClustersGPU(Atom *atom) {
sci_x[SCL_CL_X_OFFSET(atom->siclusters[sci].nclusters) + cii] = xtmp; sci_x[SCL_CL_X_OFFSET(atom->siclusters[sci].nclusters) + cii] = xtmp;
sci_x[SCL_CL_Y_OFFSET(atom->siclusters[sci].nclusters) + cii] = ytmp; sci_x[SCL_CL_Y_OFFSET(atom->siclusters[sci].nclusters) + cii] = ytmp;
sci_x[SCL_CL_Z_OFFSET(atom->siclusters[sci].nclusters) + cii] = ztmp; sci_x[SCL_CL_Z_OFFSET(atom->siclusters[sci].nclusters) + cii] = ztmp;
sci_v[SCL_CL_X_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vx[i]; sci_v[SCL_CL_X_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vx[i];
sci_v[SCL_CL_Y_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vy[i]; sci_v[SCL_CL_Y_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vy[i];
sci_v[SCL_CL_Z_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vz[i]; sci_v[SCL_CL_Z_OFFSET(atom->siclusters[sci].nclusters) + cii] = atom->vz[i];
@ -1027,6 +991,10 @@ void buildClustersGPU(Atom *atom) {
ci_x[CL_X_OFFSET + cii] = INFINITY; ci_x[CL_X_OFFSET + cii] = INFINITY;
ci_x[CL_Y_OFFSET + cii] = INFINITY; ci_x[CL_Y_OFFSET + cii] = INFINITY;
ci_x[CL_Z_OFFSET + cii] = INFINITY; ci_x[CL_Z_OFFSET + cii] = INFINITY;
sci_x[SCL_CL_X_OFFSET(atom->siclusters[sci].nclusters) + cii] = INFINITY;
sci_x[SCL_CL_Y_OFFSET(atom->siclusters[sci].nclusters) + cii] = INFINITY;
sci_x[SCL_CL_Z_OFFSET(atom->siclusters[sci].nclusters) + cii] = INFINITY;
} }
ac++; ac++;