include/gmx_ga2la.h

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  36 #ifndef _gmx_ga2la_h
  37 #define _gmx_ga2la_h
  38
  39 #include "typedefs.h"
  40 #include "smalloc.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 typedef struct {
  47     int  la;
  48     int  cell;
  49 } gmx_laa_t;
  50
  51 typedef struct {
  52     int  ga;
  53     int  la;
  54     int  cell;
  55     int  next;
  56 } gmx_lal_t;
  57
  58 typedef struct gmx_ga2la {
  59     gmx_bool      bAll;
  60     int       mod;
  61     int       nalloc;
  62     gmx_laa_t *laa;
  63     gmx_lal_t *lal;
  64     int       start_space_search;
  65 } t_gmx_ga2la;
  66
  67 /* Clear all the entries in the ga2la list */
  68 static void ga2la_clear(gmx_ga2la_t ga2la)
  69 {
  70     int i;
  71
  72     if (ga2la->bAll)
  73     {
  74         for(i=0; i<ga2la->nalloc; i++)
  75         {
  76             ga2la->laa[i].cell = -1;
  77         }
  78     }
  79     else
  80     {
  81         for(i=0; i<ga2la->nalloc; i++)
  82         {
  83             ga2la->lal[i].ga   = -1;
  84             ga2la->lal[i].next = -1;
  85         }
  86         ga2la->start_space_search = ga2la->mod;
  87     }
  88 }
  89
  90 static gmx_ga2la_t ga2la_init(int nat_tot,int nat_loc)
  91 {
  92     gmx_ga2la_t ga2la;
  93
  94     snew(ga2la,1);
  95
  96     /* There are two methods implemented for finding the local atom number
  97      * belonging to a global atom number:
  98      * 1) a simple, direct array
  99      * 2) a list of linked lists indexed with the global number modulo mod.
 100      * Memory requirements:
 101      * 1) nat_tot*2 ints
 102      * 2) nat_loc*(2+1-2(1-e^-1/2))*4 ints
 103      * where nat_loc is the number of atoms in the home + communicated zones.
 104      * Method 1 is faster for low parallelization, 2 for high parallelization.
 105      * We switch to method 2 when it uses less than half the memory method 1.
 106      */
 107     ga2la->bAll = (nat_tot < 1024 || 9*nat_loc >= nat_tot);
 108     if (ga2la->bAll)
 109     {
 110         ga2la->nalloc = nat_tot;
 111         snew(ga2la->laa,ga2la->nalloc);
 112     }
 113     else
 114     {
 115         /* Make the direct list twice as long as the number of local atoms.
 116          * The fraction of entries in the list with:
 117          * 0   size lists: e^-1/f
 118          * >=1 size lists: 1 - e^-1/f
 119          * where f is: the direct list length / #local atoms
 120          * The fraction of atoms not in the direct list is: 1-f(1-e^-1/f).
 121          */
 122         ga2la->mod = 2*nat_loc;
 123         ga2la->nalloc = over_alloc_dd(ga2la->mod);
 124         snew(ga2la->lal,ga2la->nalloc);
 125     }
 126
 127     ga2la_clear(ga2la);
 128
 129     return ga2la;
 130 }
 131
 132 /* Set the ga2la entry for global atom a_gl to local atom a_loc and cell. */
 133 static void ga2la_set(gmx_ga2la_t ga2la,int a_gl,int a_loc,int cell)
 134 {
 135     int ind,ind_prev,i;
 136
 137     if (ga2la->bAll)
 138     {
 139         ga2la->laa[a_gl].la   = a_loc;
 140         ga2la->laa[a_gl].cell = cell;
 141
 142         return;
 143     }
 144
 145     ind = a_gl % ga2la->mod;
 146
 147     if (ga2la->lal[ind].ga >= 0)
 148     {
 149         /* Search the last entry in the linked list for this index */
 150         ind_prev = ind;
 151         while(ga2la->lal[ind_prev].next >= 0)
 152         {
 153             ind_prev = ga2la->lal[ind_prev].next;
 154         }
 155         /* Search for space in the array */
 156         ind = ga2la->start_space_search;
 157         while (ind < ga2la->nalloc && ga2la->lal[ind].ga >= 0)
 158         {
 159             ind++;
 160         }
 161         /* If we are at the end of the list we need to increase the size */
 162         if (ind == ga2la->nalloc)
 163         {
 164             ga2la->nalloc = over_alloc_dd(ind+1);
 165             srenew(ga2la->lal,ga2la->nalloc);
 166             for(i=ind; i<ga2la->nalloc; i++)
 167             {
 168                 ga2la->lal[i].ga   = -1;
 169                 ga2la->lal[i].next = -1;
 170             }
 171         }
 172         ga2la->lal[ind_prev].next = ind;
 173
 174         ga2la->start_space_search = ind + 1;
 175     }
 176     ga2la->lal[ind].ga   = a_gl;
 177     ga2la->lal[ind].la   = a_loc;
 178     ga2la->lal[ind].cell = cell;
 179 }
 180
 181 /* Delete the ga2la entry for global atom a_gl */
 182 static void ga2la_del(gmx_ga2la_t ga2la,int a_gl)
 183 {
 184     int ind,ind_prev;
 185
 186     if (ga2la->bAll)
 187     {
 188         ga2la->laa[a_gl].cell = -1;
 189
 190         return;
 191     }
 192
 193     ind_prev = -1;
 194     ind = a_gl % ga2la->mod;
 195     do
 196     {
 197         if (ga2la->lal[ind].ga == a_gl)
 198         {
 199             if (ind_prev >= 0)
 200             {
 201                 ga2la->lal[ind_prev].next = ga2la->lal[ind].next;
 202
 203                 /* This index is a linked entry, so we free an entry.
 204                  * Check if we are creating the first empty space.
 205                  */
 206                 if (ind < ga2la->start_space_search)
 207                 {
 208                     ga2la->start_space_search = ind;
 209                 }
 210             }
 211             ga2la->lal[ind].ga   = -1;
 212             ga2la->lal[ind].cell = -1;
 213             ga2la->lal[ind].next = -1;
 214
 215             return;
 216         }
 217         ind_prev = ind;
 218         ind = ga2la->lal[ind].next;
 219     }
 220     while (ind >= 0);
 221
 222     return;
 223 }
 224
 225 /* Change the local atom for present ga2la entry for global atom a_gl */
 226 static void ga2la_change_la(gmx_ga2la_t ga2la,int a_gl,int a_loc)
 227 {
 228     int ind;
 229
 230     if (ga2la->bAll)
 231     {
 232         ga2la->laa[a_gl].la = a_loc;
 233
 234         return;
 235     }
 236
 237     ind = a_gl % ga2la->mod;
 238     do
 239     {
 240         if (ga2la->lal[ind].ga == a_gl)
 241         {
 242             ga2la->lal[ind].la = a_loc;
 243
 244             return;
 245         }
 246         ind = ga2la->lal[ind].next;
 247     }
 248     while (ind >= 0);
 249
 250     return;
 251 }
 252
 253 /* Returns if the global atom a_gl available locally.
 254  * Sets the local atom and cell,
 255  * cell can be larger than the number of zones,
 256  * in which case it indicates that it is more than one cell away
 257  * in zone cell - #zones.
 258  */
 259 static gmx_bool ga2la_get(const gmx_ga2la_t ga2la,int a_gl,int *a_loc,int *cell)
 260 {
 261     int ind;
 262
 263     if (ga2la->bAll)
 264     {
 265         *a_loc = ga2la->laa[a_gl].la;
 266         *cell  = ga2la->laa[a_gl].cell;
 267
 268         return (ga2la->laa[a_gl].cell >= 0);
 269     }
 270
 271     ind = a_gl % ga2la->mod;
 272     do
 273     {
 274         if (ga2la->lal[ind].ga == a_gl)
 275         {
 276             *a_loc = ga2la->lal[ind].la;
 277             *cell  = ga2la->lal[ind].cell;
 278
 279             return TRUE;
 280         }
 281         ind = ga2la->lal[ind].next;
 282     }
 283     while (ind >= 0);
 284
 285     return FALSE;
 286 }
 287
 288 /* Returns if the global atom a_gl is a home atom.
 289  * Sets the local atom.
 290  */
 291 static gmx_bool ga2la_get_home(const gmx_ga2la_t ga2la,int a_gl,int *a_loc)
 292 {
 293     int ind;
 294
 295     if (ga2la->bAll)
 296     {
 297         *a_loc = ga2la->laa[a_gl].la;
 298
 299         return (ga2la->laa[a_gl].cell == 0);
 300     }
 301
 302     ind = a_gl % ga2la->mod;
 303     do
 304     {
 305         if (ga2la->lal[ind].ga == a_gl)
 306         {
 307             if (ga2la->lal[ind].cell == 0)
 308             {
 309                 *a_loc = ga2la->lal[ind].la;
 310
 311                 return TRUE;
 312             }
 313             else
 314             {
 315                 return FALSE;
 316             }
 317         }
 318         ind = ga2la->lal[ind].next;
 319     }
 320     while (ind >= 0);
 321
 322     return FALSE;
 323 }
 324
 325 /* Returns if the global atom a_gl is a home atom.
 326  */
 327 static gmx_bool ga2la_is_home(const gmx_ga2la_t ga2la,int a_gl)
 328 {
 329     int ind;
 330
 331     if (ga2la->bAll)
 332     {
 333         return (ga2la->laa[a_gl].cell == 0);
 334     }
 335
 336     ind = a_gl % ga2la->mod;
 337     do
 338     {
 339         if (ga2la->lal[ind].ga == a_gl)
 340         {
 341             return (ga2la->lal[ind].cell == 0);
 342         }
 343         ind = ga2la->lal[ind].next;
 344     }
 345     while (ind >= 0);
 346
 347     return FALSE;
 348 }
 349
 350 #ifdef __cplusplus
 351 }
 352 #endif
 353
 354 #endif /* _gmx_ga2la_h */