1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417
|
/*
* treecode.c
* A treecode implementation to achive best scalability on shared memory machines.
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <pthread.h>
#include <assert.h>
#include <sys/time.h>
#ifndef PARALLELIZE
#define PARALLELIZE 1
#endif
#ifndef USE_MEMPOOL
#define USE_MEMPOOL 1
#endif
#define N_CHILD 8
typedef double real_t;
typedef long idx_t;
typedef unsigned long mot_t;
typedef struct vec {
double x, y, z;
} vec_t;
typedef struct mol {
idx_t id;
mot_t mid;
double mass;
vec_t acc;
vec_t pos;
vec_t vel;
} mol_t;
/* tree */
typedef struct node {
struct node *child[N_CHILD];
mol_t v_mol; /* value of node */
idx_t n_mol; /* # of mols in tree */
idx_t molarr_l, molarr_h; /* array range */
idx_t morton_l, morton_h; /* morton range */
#if USE_MEMPOOL
int ith, depth;
idx_t memp_idx;
#endif
} node_t;
/* simulation data structure */
typedef struct sim { // simulation instance
unsigned long n_mol;
int n_step;
int steps;
int depth;
mol_t *mols;
node_t *tree;
node_t **memp; /* memory pool, indexed by morton id + depth */
idx_t memp_len;
long int t_init, t_treebuild, t_treetraversal, t_treefree;
} sim_t;
sim_t sim_instance;
sim_t *sim = &sim_instance;
/* uitilities */
inline int curr_time_micro(void)
{
struct timeval tp[1];
struct timezone tzp[1];
gettimeofday(tp, tzp);
return tp->tv_sec * 1000000 + tp->tv_usec;
}
inline void * xmalloc(size_t size)
{
void *p = malloc(size);
if (p == NULL) {
perror("malloc failed");
abort();
}
return p;
}
inline void * xcmalloc(size_t size)
{
void *p = malloc(size);
if (p == NULL) {
perror("malloc failed");
abort();
}
memset(p, 0x0, size);
return p;
}
/* tree routines */
inline node_t * memp_get(idx_t idx)
{
node_t *ptr = sim->memp[idx];
if (ptr) {
sim->memp[idx] = NULL;
} else {
ptr = xmalloc(sizeof(node_t));
memset(ptr, 0x0, sizeof(node_t));
ptr->memp_idx = idx;
}
return ptr;
}
inline void memp_put(node_t * ptr)
{
idx_t idx = ptr->memp_idx;
if (sim->memp[idx]) {
printf("warning: memory pool put failed for %ld\n", idx);
} else {
sim->memp[idx] = ptr;
}
}
inline int bin_search(mol_t *mols, mot_t key,
idx_t imin, idx_t imax, int low_bound)
{
idx_t imid;
while (imax >= imin) {
imid = (imin + imax) / 2;
if (mols[imid].mid < key)
imin = imid + 1;
else if (mols[imid].mid > key)
imax = imid - 1;
else
return imid;
}
return low_bound ? imin : imax;
}
// Given ml and mh, find a subrange [il, ih] from original [il, ih]
int select_subarr(mol_t *mols, mot_t ml, mot_t mh, idx_t *il, idx_t *ih)
{
idx_t _low, _high;
if (mols[*ih].mid < ml || mols[*il].mid > mh) return 1;
if ((_low = bin_search(mols, ml, *il, *ih, 1)) == -1) return 1;
if ((_high = bin_search(mols, mh, *il, *ih, 0)) == -1) return 1;
if (_low > _high) return 1;
*il = _low;
*ih = _high;
return 0;
}
void tree_build_serial(node_t * node)
{
idx_t curr_il, curr_ih;
mot_t curr_ml, curr_mh;
real_t stride;
mol_t * mols;
int i;
mols = sim->mols;
if (node->n_mol == 1) {
node->v_mol = mols[node->molarr_l];
} else if (node->n_mol > 1) {
stride = (node->morton_h - node->morton_l) / N_CHILD;
curr_il = node->molarr_l;
curr_ih = node->molarr_h;
for (i = 0; i < N_CHILD; i++) {
curr_ml = node->morton_l + stride * i + i;
curr_mh = curr_ml + stride;
if (select_subarr(mols, curr_ml, curr_mh, &curr_il, &curr_ih) == 0) {
/* subspaces is non-empty */
node->child[i] = xcmalloc(sizeof(node_t));
node->child[i]->n_mol = curr_ih - curr_il + 1; /* assert(n_mol>0) */
node->child[i]->molarr_l = curr_il;
node->child[i]->molarr_h = curr_ih;
node->child[i]->morton_l = curr_ml;
node->child[i]->morton_h = curr_mh;
curr_il = curr_ih;
tree_build_serial(node->child[i]);
} else {
curr_il = node->molarr_l;
}
curr_ih = node->molarr_h;
}
}
}
void * tree_build_parallel(void *args)
{
pthread_t ths[N_CHILD];
idx_t curr_il, curr_ih, base, offset, ith;
mot_t curr_ml, curr_mh;
real_t stride;
mol_t * mols;
node_t * node;
int i, n_ths, curr_depth;
n_ths = 0;
mols = sim->mols;
node = (node_t *) args;
if (node->n_mol == 1) {
node->v_mol = mols[node->molarr_l];
} else if (node->n_mol > 1) {
stride = (node->morton_h - node->morton_l) / N_CHILD;
curr_il = node->molarr_l;
curr_ih = node->molarr_h;
#if USE_MEMPOOL
curr_depth = node->depth + 1;
base = (pow(N_CHILD, curr_depth) - 1) / (N_CHILD - 1);
offset = node->ith * N_CHILD;
#endif
for (i = 0; i < N_CHILD; i++) {
curr_ml = node->morton_l + stride * i + i;
curr_mh = curr_ml + stride;
if (select_subarr(mols, curr_ml, curr_mh, &curr_il, &curr_ih) == 0) {
/* subspaces is non-empty */
#if USE_MEMPOOL
ith = offset + i;
node->child[i] = memp_get(base + ith);
node->child[i]->ith = ith;
node->child[i]->depth = curr_depth;
#else
node->child[i] = xcmalloc(sizeof(node_t));
#endif
node->child[i]->n_mol = curr_ih - curr_il + 1; /* assert(n_mol>0) */
node->child[i]->molarr_l = curr_il;
node->child[i]->molarr_h = curr_ih;
node->child[i]->morton_l = curr_ml;
node->child[i]->morton_h = curr_mh;
curr_il = curr_ih;
pthread_create(&ths[n_ths], NULL, tree_build_parallel, node->child[i]);
n_ths++;
} else {
curr_il = node->molarr_l;
}
curr_ih = node->molarr_h;
}
}
for (i = 0; i < n_ths; i++)
pthread_join(ths[i], NULL);
}
void tree_build(void)
{
node_t * root;
sim->t_treebuild = curr_time_micro();
#if USE_MEMPOOL
root = memp_get(0);
root->ith = 0;
root->depth = 0;
root->memp_idx = 0;
#else
root = (node_t *) xcmalloc(sizeof(node_t));
#endif
root->n_mol = sim->n_mol;
root->molarr_l = 0;
root->molarr_h = sim->n_mol - 1;
root->morton_l = sim->mols[root->molarr_l].mid;
root->morton_h = sim->mols[root->molarr_h].mid;
sim->tree = root;
#if PARALLELIZE
tree_build_parallel(sim->tree);
#else
tree_build_serial(sim->tree);
#endif
sim->t_treebuild = curr_time_micro() - sim->t_treebuild;
}
void tree_free_serial(node_t * node)
{
int i;
if (node == NULL) return;
for (i=0; i < N_CHILD; i++)
tree_free_serial(node->child[i]);
free(node);
}
void * tree_free_parallel(void * args)
{
pthread_t ths[N_CHILD];
node_t *p = (node_t *) args;
int i;
if (p == NULL) return (void *) 0;
for (i = 0; i < N_CHILD; i++) {
if (i < N_CHILD - 1)
pthread_create(&ths[i], NULL, tree_free_parallel, p->child[i]);
else
tree_free_parallel(p->child[i]);
}
for (i = 0; i < N_CHILD - 1; i++)
pthread_join(ths[i], NULL);
#if USE_MEMPOOL
memp_put(p);
#else
free(p);
#endif
}
void tree_free(void)
{
sim->t_treefree = curr_time_micro();
#if PARALLELIZE
tree_free_parallel(sim->tree);
#else
tree_free_serial(sim->tree);
#endif
sim->t_treefree = curr_time_micro() - sim->t_treefree;
}
void tree_check_walk(node_t *node, int *n, int depth) {
int i;
if (node == NULL) return;
(*n)++;
for (i = 0; i < N_CHILD; i++) {
tree_check_walk(node->child[i], n, depth + 1);
}
}
void tree_valid_check(void)
{
int n_total = 0;
sim->t_treetraversal = curr_time_micro();
tree_check_walk(sim->tree, &n_total, 0);
sim->t_treetraversal = curr_time_micro() - sim->t_treetraversal;
if (n_total != (pow(N_CHILD, sim->depth + 1) - 1) / (N_CHILD - 1))
printf(" valid check failed: walked %d nodes\n", n_total);
}
/* simulation routines */
void init(int argc, char *argv[])
{
idx_t i;
curr_time_micro(); /* dummy call to make first timing accurate, Darwin only? */
if (argc < 3) {
printf("usage: %s DEPTH STEPS\n", argv[0]);
exit(0);
}
sim->depth = atoi(argv[1]);
sim->n_step = atoi(argv[2]);
sim->n_mol = pow(N_CHILD, sim->depth);
sim->steps = 0;
sim->t_treebuild = 0;
sim->mols = xmalloc(sizeof(mol_t) * sim->n_mol);
for (i = 0; i < sim->n_mol; i++) {
sim->mols[i].id = i;
sim->mols[i].mid = i;
}
#if USE_MEMPOOL
sim->memp_len = (pow(N_CHILD, sim->depth + 1) - 1) / (N_CHILD - 1);
sim->memp = xmalloc(sizeof(node_t *) * sim->memp_len);
memset(sim->memp, 0x0, sizeof(node_t *) * sim->memp_len);
printf("N=%ld, STEPS=%d, MEMPOOL=%ld\n",
sim->n_mol, sim->n_step, sim->memp_len);
#else
printf("N=%ld, STEPS=%d\n", sim->n_mol, sim->n_step);
#endif
}
void finalize(void)
{
idx_t i;
free(sim->mols);
#if USE_MEMPOOL
for (i = 0; i < sim->memp_len; i++)
free(sim->memp[i]);
free(sim->memp);
#endif
}
void status(void)
{
fprintf(stdout, "[%03d] TreeBuild: %ld, TreeTraveral: %ld, TreeFree: %ld\n", sim->steps,
sim->t_treebuild, sim->t_treetraversal, sim->t_treefree);
}
int main(int argc, char *argv[])
{
init(argc, argv);
while (sim->steps < sim->n_step) {
tree_build();
tree_valid_check();
tree_free();
status();
sim->steps++;
}
finalize();
return 0;
}
|