/* attach constraints to bodies after reading */
static void dom_attach_constraints (DOM *dom)
{
BODY *bod;
CON *con;
for (bod = dom->bod; bod; bod = bod->next) SET_Free (&dom->setmem, &bod->con);
for (con = dom->con; con; con = con->next)
{
if (con->master)
{
ASSERT_DEBUG (MAP_Find_Node (dom->idb, (void*) (long) con->master->id, NULL), "Invalid master id");
SET_Insert (&dom->setmem, &con->master->con, con, NULL);
}
if (con->slave)
{
ASSERT_DEBUG (MAP_Find_Node (dom->idb, (void*) (long) con->slave->id, NULL), "Invalid slave id");
SET_Insert (&dom->setmem, &con->slave->con, con, NULL);
}
}
}
/* pick leaves overlapping the extents */
void KDT_Pick_Extents (KDT *kd, double *extents, SET **leaves)
{
if (kd->d < 0) /* leaf */
{
SET_Insert (NULL, leaves, kd, NULL);
}
else if (extents [kd->d+3] <= kd->p [kd->d]) KDT_Pick_Extents (kd->l, extents, leaves);
else if (extents [kd->d] > kd->p [kd->d]) KDT_Pick_Extents (kd->r, extents, leaves);
else
{
KDT_Pick_Extents (kd->l, extents, leaves);
KDT_Pick_Extents (kd->r, extents, leaves);
}
}
/* receive reactions updated by middle nodes */
static void receive_middle_reactions (DOM *dom, COMDATA *recv, int nrecv, MEM *setmem, SET **midupd)
{
COMDATA *ptr;
int i, j, *k;
CON *con;
for (i = 0, ptr = recv; i < nrecv; i ++, ptr ++)
{
for (j = 0, k = ptr->i; j < ptr->ints; j ++, k ++)
{
ASSERT_DEBUG_EXT (con = MAP_Find (dom->conext, (void*) (long) (*k), NULL), "Invalid constraint id");
SET_Insert (setmem, midupd, con, NULL);
}
}
}
/* read domain state */
void dom_read_state (DOM *dom, PBF *bf)
{
BODY *bod, *next;
int ncon;
/* clear contacts */
MAP_Free (&dom->mapmem, &dom->idc);
MEM_Release (&dom->conmem);
dom->con = NULL;
dom->ncon = 0;
/* read all bodies if needed */
if (!dom->allbodiesread) read_new_bodies (dom, bf);
/* mark all bodies as absent */
for (bod = dom->bod; bod; bod = bod->next) bod->flags |= BODY_ABSENT;
SET *usedlabel = NULL;
for (; bf; bf = bf->next)
{
if (PBF_Label (bf, "DOM"))
{
/* read iover */
int iover = 2;
if (PBF_Label (bf, "IOVER"))
{
PBF_Int (bf, &iover, 1);
}
/* read time step */
ASSERT (PBF_Label (bf, "STEP"), ERR_FILE_FORMAT);
PBF_Double (bf, &dom->step, 1);
/* read constraints merit */
ASSERT (PBF_Label (bf, "MERIT"), ERR_FILE_FORMAT);
PBF_Double (bf, &dom->merit, 1);
/* read body states */
ASSERT (PBF_Label (bf, "BODS"), ERR_FILE_FORMAT);
int nbod;
PBF_Int (bf, &nbod, 1);
for (int n = 0; n < nbod; n ++)
{
unsigned int id;
PBF_Uint (bf, &id, 1);
bod = MAP_Find (dom->idb, (void*) (long) id, NULL);
if (bod == NULL) /* pick from all bodies set */
{
ASSERT_DEBUG_EXT (bod = MAP_Find (dom->allbodies, (void*) (long) id, NULL), "Body id invalid");
if (bod->label)
{
MAP *node = MAP_Find_Node (dom->lab, bod->label, (MAP_Compare)strcmp);
if (node)
{
node->data = bod; /* body fregments can inherit labels */
SET_Insert (NULL, &usedlabel, bod->label, (SET_Compare)strcmp);
}
else MAP_Insert (&dom->mapmem, &dom->lab, bod->label, bod, (MAP_Compare) strcmp);
}
MAP_Insert (&dom->mapmem, &dom->idb, (void*) (long) bod->id, bod, NULL);
bod->next = dom->bod;
if (dom->bod) dom->bod->prev = bod;
dom->bod = bod;
bod->dom = dom;
dom->nbod ++;
}
BODY_Read_State (bod, bf, iover);
bod->flags &= ~BODY_ABSENT;
}
/* read constraints */
ASSERT (PBF_Label (bf, "CONS"), ERR_FILE_FORMAT);
PBF_Int (bf, &ncon, 1);
for (int n = 0; n < ncon; n ++)
{
CON *con;
con = read_constraint (dom, iover, bf);
MAP_Insert (&dom->mapmem, &dom->idc, (void*) (long) con->id, con, NULL);
con->next = dom->con;
if (dom->con) dom->con->prev = con;
dom->con = con;
}
dom->ncon += ncon;
}
}
/* remove absent bodies */
for (bod = dom->bod; bod; bod = next)
{
next = bod->next;
if (bod->flags & BODY_ABSENT)
{
if (bod->label && !SET_Contains (usedlabel, bod->label, (SET_Compare)strcmp))
MAP_Delete (&dom->mapmem, &dom->lab, bod->label, (MAP_Compare) strcmp);
MAP_Delete (&dom->mapmem, &dom->idb, (void*) (long) bod->id, NULL);
if (bod->next) bod->next->prev = bod->prev;
if (bod->prev) bod->prev->next = bod->next;
else dom->bod = bod->next;
dom->nbod --;
}
}
SET_Free (NULL, &usedlabel);
/* attach constraints to bodies */
dom_attach_constraints (dom);
}
/* create rank coloring using adjacency graph between processors derived from the W graph */
static int* processor_coloring (GAUSS_SEIDEL *gs, LOCDYN *ldy)
{
int i, n, m, ncpu, rank, *color, *size, *disp, *adj;
SET *adjcpu, *item;
MEM setmem;
DIAB *dia;
OFFB *blk;
CON *con;
adjcpu = NULL;
rank = ldy->dom->rank;
ncpu = ldy->dom->ncpu;
MEM_Init (&setmem, sizeof (SET), 128);
ERRMEM (color = MEM_CALLOC (ncpu * sizeof (int)));
ERRMEM (disp = malloc (sizeof (int [ncpu + 1])));
ERRMEM (size = malloc (sizeof (int [ncpu])));
/* collaps W adjacency into processor adjacency */
for (dia = ldy->dia; dia; dia = dia->n)
{
for (blk = dia->adjext; blk; blk = blk->n)
{
con = (CON*) blk->dia;
SET_Insert (&setmem, &adjcpu, (void*) (long) con->rank, NULL);
}
}
n = SET_Size (adjcpu);
MPI_Allgather (&n, 1, MPI_INT, size, 1, MPI_INT, MPI_COMM_WORLD);
for (i = disp [0] = 0; i < ncpu - 1; i ++) disp [i+1] = disp [i] + size [i];
for (i = 0, item = SET_First (adjcpu); item; i ++, item = SET_Next (item)) color [i] = (int) (long) item->data;
m = disp [ncpu] = (disp [ncpu-1] + size [ncpu-1]);
ERRMEM (adj = malloc (sizeof (int [m])));
MPI_Allgatherv (color, n, MPI_INT, adj, size, disp, MPI_INT, MPI_COMM_WORLD); /* gather graph adjacency */
for (i = 0; i < ncpu; i ++) color [i] = 0; /* zero colors */
for (i = 0; i < ncpu; i ++) /* simple BFS coloring */
{
int *j, *k;
do
{
color [i] ++; /* start from first color */
for (j = &adj[disp[i]], k = &adj[disp[i+1]]; j < k; j ++) /* for each adjacent vertex */
{
if (color [*j] == color [i]) break; /* see whether the trial color exists in the adjacency */
}
}
while (j < k); /* if so try next color */
}
for (m = i = 0; i < ncpu; i ++) m = MAX (m, color [i]); /* compute number of colors */
gs->colors = m; /* record number of colors */
if (rank == 0 && ldy->dom->verbose && gs->verbose)
{
#if DEBUG
for (i = 0; i < ncpu; i ++)
{
int *j, *k;
printf ("GAUSS_SEIDEL: RANK %d [%d] ADJCPU:", i, color [i]);
for (j = &adj[disp[i]], k = &adj[disp[i+1]]; j < k; j ++) printf (" %d [%d]", *j, color [*j]);
printf ("\n");
}
#endif
printf ("GAUSS_SEIDEL: PROCESSOR COLORS = %d\n", m);
}
MEM_Release (&setmem);
free (size);
free (disp);
free (adj);
return color;
}
static void overlap (void *data, BOX *one, BOX *two)
{
SET_Insert (NULL, (SET**)&one->body, two, NULL);
SET_Insert (NULL, (SET**)&two->body, one, NULL);
}