diff --git a/src/fof.c b/src/fof.c
index dcae2e1569180064e1c965d8640310041889257b..a3282615869e422cb213954b0cd95083241aa70e 100644
--- a/src/fof.c
+++ b/src/fof.c
@@ -288,7 +288,7 @@ static void rec_fof_search_pair_foreign(struct cell *ci, struct cell *cj, struct
/* Perform FOF search between pairs of cells that are within the linking
* length and not the same cell. */
else if (ci != cj)
- fof_search_pair_cells_foreign_new(s, ci, cj, send_count, fof_send);
+ fof_search_pair_cells_foreign(s, ci, cj, send_count, fof_send);
else if (ci == cj) error("Pair FOF called on same cell!!!");
}
@@ -511,163 +511,6 @@ void fof_search_pair_cells_foreign(struct space *s, struct cell *ci, struct cell
const int periodic = s->periodic;
double diff[3];
- if(ci_local) {
-
- for (int k = 0; k < 3; k++) {
- diff[k] = cj->loc[k] - ci->loc[k];
- if (periodic && diff[k] < -dim[k] / 2)
- shift[k] = dim[k];
- else if (periodic && diff[k] > dim[k] / 2)
- shift[k] = -dim[k];
- else
- shift[k] = 0.0;
- diff[k] += shift[k];
- }
-
- /* Loop over particles and find which particles belong in the same group. */
- for (size_t i = 0; i < count_i; i++) {
-
- struct gpart *pi = &gparts_i[i];
- const double pix = pi->x[0] - shift[0];
- const double piy = pi->x[1] - shift[1];
- const double piz = pi->x[2] - shift[2];
-
- /* Find the root of pi. */
- int root_i = fof_find(offset_i[i] - node_offset, group_index);
-
- for (size_t j = 0; j < count_j; j++) {
-
- struct gpart *pj = &gparts_j[j];
- const double pjx = pj->x[0];
- const double pjy = pj->x[1];
- const double pjz = pj->x[2];
-
- /* Compute pairwise distance, remembering to account for boundary
- * conditions. */
- float dx[3], r2 = 0.0f;
- dx[0] = pix - pjx;
- dx[1] = piy - pjy;
- dx[2] = piz - pjz;
-
- for (int k = 0; k < 3; k++) r2 += dx[k] * dx[k];
-
- /* Hit or miss? */
- if (r2 < l_x2) {
- //message("Particle %lld in range of foreign particle %lld. Group ID: %d root_i: %d", pi->id_or_neg_offset, pj->id_or_neg_offset, group_index[root_i - node_offset], root_i);
-
- /* Store the particle IDs and group ID for communication. */
- fof_send[*send_count].local_pid = pi->id_or_neg_offset;
- fof_send[*send_count].foreign_pid = pj->id_or_neg_offset;
- fof_send[*send_count].root_i = root_i;
- (*send_count)++;
- local_send_count++;
-
- //fprintf(fof_file, " %7zu %7zu %7d\n", pi->id_or_neg_offset, pj->id_or_neg_offset, root_i);
- }
- }
- }
-
- }
-
- if(cj_local) {
-
- for (int k = 0; k < 3; k++) {
- diff[k] = ci->loc[k] - cj->loc[k];
- if (periodic && diff[k] < -dim[k] / 2)
- shift[k] = dim[k];
- else if (periodic && diff[k] > dim[k] / 2)
- shift[k] = -dim[k];
- else
- shift[k] = 0.0;
- diff[k] += shift[k];
- }
-
- /* Loop over particles and find which particles belong in the same group. */
- for (size_t j = 0; j < count_j; j++) {
-
- struct gpart *pj = &gparts_j[j];
- const double pjx = pj->x[0] - shift[0];
- const double pjy = pj->x[1] - shift[1];
- const double pjz = pj->x[2] - shift[2];
-
- /* Find the root of pj. */
- int root_j = fof_find(offset_j[j] - node_offset, group_index);
-
- for (size_t i = 0; i < count_i; i++) {
-
- struct gpart *pi = &gparts_i[i];
- const double pix = pi->x[0];
- const double piy = pi->x[1];
- const double piz = pi->x[2];
-
- /* Compute pairwise distance, remembering to account for boundary
- * conditions. */
- float dx[3], r2 = 0.0f;
- dx[0] = pjx - pix;
- dx[1] = pjy - piy;
- dx[2] = pjz - piz;
-
- for (int k = 0; k < 3; k++) r2 += dx[k] * dx[k];
-
- /* Hit or miss? */
- if (r2 < l_x2) {
-
- //message("Particle %lld in range of foreign particle %lld. Group ID: %d root_j: %d", pj->id_or_neg_offset, pi->id_or_neg_offset, group_index[root_j - node_offset], root_j);
- /* Store the particle IDs and group ID for communication. */
- fof_send[*send_count].local_pid = pj->id_or_neg_offset;
- fof_send[*send_count].foreign_pid = pi->id_or_neg_offset;
- fof_send[*send_count].root_i = root_j;
- (*send_count)++;
- local_send_count++;
- //fprintf(fof_file, " %7zu %7zu %7d\n", pj->id_or_neg_offset, pi->id_or_neg_offset, root_j);
- }
- }
- }
-
- }
-
- //if(local_send_count > 0) {
-
- // if(ci_local)
- // message("Rank: %d sending %zu links to rank %d for testing. ci: (%lf,%lf,%lf) -> cj: (%lf,%lf,%lf).", engine_rank, local_send_count, cj->nodeID, ci->loc[0], ci->loc[1], ci->loc[2], cj->loc[0], cj->loc[1], cj->loc[2]);
- //
- // if(cj_local)
- // message("Rank: %d sending %zu links to rank %d for testing. cj: (%lf,%lf,%lf) -> ci: (%lf,%lf,%lf).", engine_rank, local_send_count, ci->nodeID, cj->loc[0], cj->loc[1], cj->loc[2], ci->loc[0], ci->loc[1], ci->loc[2]);
- //}
-
-}
-
-/* Perform a FOF search between a local and foreign cell using the Union-Find algorithm.
- * Communicate any links found between particles to the appropriate node.*/
-void fof_search_pair_cells_foreign_new(struct space *s, struct cell *ci, struct cell *cj, size_t *send_count, struct fof_mpi *fof_send ) {
-
- const size_t count_i = ci->gcount;
- const size_t count_j = cj->gcount;
- struct gpart *gparts_i = ci->gparts;
- struct gpart *gparts_j = cj->gparts;
- const double dim[3] = {s->dim[0], s->dim[1], s->dim[2]};
- const double l_x2 = s->l_x2;
- int *group_index = s->fof_data.group_index;
-
- /* Make a list of particle offsets into the global gparts array. */
- int *const offset_i = group_index + (ptrdiff_t)(gparts_i - s->gparts);
- int *const offset_j = group_index + (ptrdiff_t)(gparts_j - s->gparts);
-
- /* Account for boundary conditions.*/
- double shift[3] = {0.0, 0.0, 0.0};
-
- /* Check whether cells are local to the node. */
- const int ci_local = (ci->nodeID == engine_rank);
- const int cj_local = (cj->nodeID == engine_rank);
-
- if((ci_local && cj_local) || (!ci_local && !cj_local)) error("FOF search of foreign cells called on two local cells or two foreign cells.");
-
- size_t local_send_count = 0;
-
- /* Get the relative distance between the pairs, wrapping. */
- const int periodic = s->periodic;
- double diff[3];
-
if(ci_local) {
for (int k = 0; k < 3; k++) {
@@ -984,6 +827,8 @@ void fof_search_tree_mapper(void *map_data, int num_elements,
*/
void fof_search_foreign_cells(struct space *s) {
+#ifdef WITH_MPI
+
struct engine *e = s->e;
struct cell *cells = s->cells_top;
int *group_index = s->fof_data.group_index;
@@ -1067,8 +912,6 @@ void fof_search_foreign_cells(struct space *s) {
/* Skip empty cells. */
if(foreign_cell->gcount == 0) continue;
- //rec_fof_search_pair_foreign(local_cell, foreign_cell, s, dim, search_r2, &send_count, fof_send);
-
/* Check if local cell has already been added to the local list of cells. */
if(!found) {
const double r2 = cell_min_dist(local_cell, foreign_cell, dim);
@@ -1108,17 +951,21 @@ void fof_search_foreign_cells(struct space *s) {
for(int i=0; i<sched->nr_tasks; i++) {
- if(tasks[i].type == task_type_send) {
- scheduler_activate(sched,&tasks[i]);
+ struct task *t = &tasks[i];
+
+ if(t->type == task_type_send && t->subtype == task_subtype_gpart) {
+ scheduler_activate(sched,t);
nr_sends++;
}
- if(tasks[i].type == task_type_recv) {
- scheduler_activate(sched,&tasks[i]);
+ if(t->type == task_type_recv && t->subtype == task_subtype_gpart) {
+ scheduler_activate(sched,t);
nr_recvs++;
}
}
-
+
+ message("Rank %d. No. of sends activated: %d, no. of receives activated: %d", engine_rank, nr_sends, nr_recvs);
+
engine_launch(e);
for(int i=0; i<e->nr_proxies; i++) {
@@ -1127,14 +974,23 @@ void fof_search_foreign_cells(struct space *s) {
struct cell *restrict foreign_cell = e->proxies[i].cells_in[j];
struct gpart *gparts = foreign_cell->gparts;
-
+
+ if(foreign_cell->nodeID == engine_rank) error("Rank %d. Foreign cell is actually local.", engine_rank);
+
+ if(gparts[0].root >= node_offset && gparts[0].root < node_offset + s->nr_gparts) {
+ //error("Rank %d received foreign particle with local root: %d", engine_rank, gparts[k].root);
+ message("Rank %d received foreign particle %lld from rank %d with a local root: %d. i=%d,j=%d.", engine_rank, gparts[0].id_or_neg_offset, foreign_cell->nodeID, gparts[0].root, i, j);
+ }
for(int k=0; k<foreign_cell->gcount; k++) {
- if(gparts[k].root >= node_offset && gparts[k].root < node_offset + s->nr_gparts) error("Rank %d received foreign particle with local root: %d", engine_rank, gparts[k].root);
+ if(gparts[k].root >= node_offset && gparts[k].root < node_offset + s->nr_gparts) {
+ //error("Rank %d received foreign particle with local root: %d", engine_rank, gparts[k].root);
+ //message("Rank %d received foreign particle %lld from rank %d with a local root: %d. i=%d,j=%d,k=%d.", engine_rank, gparts[k].id_or_neg_offset, foreign_cell->nodeID, gparts[k].root, i, j, k);
+ }
}
}
}
- size_t link_count_new = 0;
+ size_t link_count = 0;
for(int i=0; i<interface_cell_count; i++) {
@@ -1152,27 +1008,29 @@ void fof_search_foreign_cells(struct space *s) {
/* Skip empty cells. */
if(foreign_cell->gcount == 0) continue;
- rec_fof_search_pair_foreign(local_cell, foreign_cell, s, dim, search_r2, &link_count_new, fof_send);
+ rec_fof_search_pair_foreign(local_cell, foreign_cell, s, dim, search_r2, &link_count, fof_send);
}
}
}
- message("Rank %d found %zu links between local and foreign groups.", engine_rank, link_count_new);
+ message("Rank %d found %zu links between local and foreign groups.", engine_rank, link_count);
struct fof_mpi *fof_list;
int list_count = 0;
if (posix_memalign((void**)&fof_list, SWIFT_STRUCT_ALIGNMENT,
- link_count_new * sizeof(struct fof_mpi)) != 0)
+ link_count * sizeof(struct fof_mpi)) != 0)
error("Error while allocating memory for FOF MPI communication");
- for(int i=0; i<link_count_new; i++) {
+ for(int i=0; i<link_count; i++) {
int found = 0;
int local_root = fof_send[i].local_pid;
int foreign_root = fof_send[i].foreign_pid;
+ if(local_root == foreign_root) error("Particles have same root. local_root: %d, foreign_root: %d", local_root, foreign_root);
+
for(int j=0; j<list_count; j++) {
if(fof_list[j].local_pid == local_root && fof_list[j].foreign_pid == foreign_root) {
found = 1;
@@ -1193,6 +1051,13 @@ void fof_search_foreign_cells(struct space *s) {
int global_list_count = 0;
MPI_Allreduce(&list_count, &global_list_count, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+
+ int *list_counts = NULL;
+ if (posix_memalign((void**)&list_counts, SWIFT_STRUCT_ALIGNMENT,
+ e->nr_nodes * sizeof(int)) != 0)
+ error("Error while allocating memory for FOF MPI communication");
+
+ MPI_Allgather(&list_count, 1, MPI_INT, list_counts, 1, MPI_INT, MPI_COMM_WORLD);
message("Global list count: %d", global_list_count);
@@ -1204,13 +1069,23 @@ void fof_search_foreign_cells(struct space *s) {
global_list_count * sizeof(struct fof_mpi)) != 0)
error("Error while allocating memory for FOF MPI communication");
- MPI_Allgather(fof_list, list_count, fof_mpi_type, global_fof_list, list_count, fof_mpi_type, MPI_COMM_WORLD);
+ int *displ = NULL;
+ if (posix_memalign((void**)&displ, SWIFT_STRUCT_ALIGNMENT,
+ e->nr_nodes * sizeof(int)) != 0)
+ error("Error while allocating memory for FOF MPI communication");
+
+ displ[0] = 0;
+ for(int i=1; i<e->nr_nodes; i++) displ[i] = displ[i-1] + list_counts[i-1];
+
+ MPI_Allgatherv(fof_list, list_count, fof_mpi_type, global_fof_list, list_counts, displ, fof_mpi_type, MPI_COMM_WORLD);
for(int i=0; i<global_list_count; i++) {
fprintf(fof_file, " %7lld <-> %7lld\n", global_fof_list[i].local_pid, global_fof_list[i].foreign_pid);
//message("Rank %d. Global FOF list: %lld <-> %lld", engine_rank, global_fof_list[i].local_pid, global_fof_list[i].foreign_pid);
}
+ fclose(fof_file);
+
for(int i=0; i<global_list_count; i++) {
global_fof_list_offset[i].local_pid = i;
global_fof_list_offset[i].foreign_pid = i;
@@ -1219,50 +1094,49 @@ void fof_search_foreign_cells(struct space *s) {
for(int i=0; i<global_list_count; i++) {
int group_i = global_fof_list[i].local_pid;
int group_j = global_fof_list[i].foreign_pid;
+
+ //if((group_j >= node_offset && group_j < node_offset + s->nr_gparts)) {
+ // int root = fof_find(group_j - node_offset, group_index);
- int min_root = min(group_i, group_j);
+ // group_j = root;
- //if(group_j < group_i) {
-
- //min_root = group_j;
+ //}
+ //
+ //if((group_i >= node_offset && group_i < node_offset + s->nr_gparts)) {
+ // int root = fof_find(group_i - node_offset, group_index);
- for(int j=i + 1; j<global_list_count; j++) {
- int root_i = global_fof_list[j].local_pid;
- int root_j = global_fof_list[j].foreign_pid;
+ // group_i = root;
- if(root_i == group_j) {
- if(root_j < min_root) min_root = root_j;
- }
- else if(root_j == group_j) {
- if(root_i < min_root) min_root = root_i;
- }
- }
+ //}
- //if( group_i >= node_offset && group_i < node_offset + s->nr_gparts) {
- // message("Rank %d. Group %d links to %d.", engine_rank,group_i, min_root);
- //}
+ if(group_i == group_j) error("Particles have same root. local_root: %d, foreign_root: %d", group_i, group_j);
- //}
- //else {
- //min_root = group_i;
-
- for(int j=i + 1; j<global_list_count; j++) {
- int root_i = global_fof_list[j].local_pid;
- int root_j = global_fof_list[j].foreign_pid;
+ int min_root = min(group_i, group_j);
- if(root_i == group_i) {
- if(root_j < min_root) min_root = root_j;
- }
- else if(root_j == group_i) {
- if(root_i < min_root) min_root = root_i;
- }
+ for(int j=i + 1; j<global_list_count; j++) {
+ int root_i = global_fof_list[j].local_pid;
+ int root_j = global_fof_list[j].foreign_pid;
+
+ if(root_i == group_j) {
+ if(root_j < min_root) min_root = root_j;
+ }
+ else if(root_j == group_j) {
+ if(root_i < min_root) min_root = root_i;
+ }
+ }
+
+ for(int j=i + 1; j<global_list_count; j++) {
+ int root_i = global_fof_list[j].local_pid;
+ int root_j = global_fof_list[j].foreign_pid;
+
+ if(root_i == group_i) {
+ if(root_j < min_root) min_root = root_j;
+ }
+ else if(root_j == group_i) {
+ if(root_i < min_root) min_root = root_i;
}
+ }
- //if( group_j >= node_offset && group_j < node_offset + s->nr_gparts) {
- // message("Rank %d. Group %d links to %d.", engine_rank, group_j, min_root);
- //}
- //}
-
if(((group_j >= node_offset && group_j < node_offset + s->nr_gparts) ||
(group_i >= node_offset && group_i < node_offset + s->nr_gparts) ) &&
(group_i != min_root && group_j != min_root) ) {
@@ -1272,21 +1146,60 @@ void fof_search_foreign_cells(struct space *s) {
if((group_j >= node_offset && group_j < node_offset + s->nr_gparts) &&
(group_j != min_root)) {
int root = fof_find(group_j - node_offset, group_index);
+ if(root != group_j) message("Rank %d. The root of group_j has changed from: %d to %d", engine_rank, group_j, root);
+ //message("Rank %d. Updating local root: %d to: %d", engine_rank, root, min_root);
+
+ if(root < min_root) message("Rank %d. Group_j: %d Trying to set a root: %d to a larger value: %d", engine_rank, group_j, root, min_root);
+
+ /* Check root is local to node. */
+ if(root >= node_offset && root < node_offset + s->nr_gparts) {
+ if(root > min_root) {
+ group_index[root - node_offset] = min_root;
+ }
+ else if(min_root >= node_offset && min_root < node_offset + s->nr_gparts){
+
+ int root_new = fof_find(min_root - node_offset, group_index);
+ //if(min_root != root_new) error("Wrong min_root used. min_root in fof_list: %d and actual root found in group_index: %d", min_root, root_new);
+
+ group_index[root_new - node_offset] = root;
- group_index[root - node_offset] = min_root;
+ }
+ }
}
if((group_i >= node_offset && group_i < node_offset + s->nr_gparts) &&
(group_i != min_root)) {
int root = fof_find(group_i - node_offset, group_index);
+ if(root != group_i) message("Rank %d. The root of group_i has changed from: %d to %d", engine_rank, group_i, root);
+
+ //message("Rank %d. Updating local root: %d to: %d", engine_rank, root, min_root);
+
+ if(root < min_root) message("Rank %d. Group_i: %d Trying to set a root: %d to a larger value: %d", engine_rank, group_i, root, min_root);
+
+ /* Check root is local to node. */
+ if(root >= node_offset && root < node_offset + s->nr_gparts) {
+ if(root > min_root) {
+ group_index[root - node_offset] = min_root;
+ }
+ else if(min_root >= node_offset && min_root < node_offset + s->nr_gparts){
+
+ int root_new = fof_find(min_root - node_offset, group_index);
+ //if(min_root != root_new) error("Wrong min_root used. min_root in fof_list: %d and actual root found in group_index: %d", min_root, root_new);
- group_index[root - node_offset] = min_root;
+ group_index[root_new - node_offset] = root;
+
+ }
+ }
}
+
+ //if(engine_rank == 0) message("Rank 0. Updating local roots. %d of %d....", i, global_list_count);
//global_fof_list[i].local_pid = min_root;
//global_fof_list[i].foreign_pid = min_root;
}
- fclose(fof_file);
+ message("Rank %d finished linking local roots to foreign roots.", engine_rank);
+
+#endif /* WITH_MPI */
}
@@ -1321,9 +1234,11 @@ void fof_search_tree(struct space *s) {
bzero(global_nr_gparts, s->e->nr_nodes * sizeof(int));
- MPI_Allgather(&s->nr_gparts, 1, MPI_INT, global_nr_gparts, s->e->nr_nodes - 1, MPI_INT, MPI_COMM_WORLD);
+ MPI_Allgather(&s->nr_gparts, 1, MPI_INT, global_nr_gparts, 1, MPI_INT, MPI_COMM_WORLD);
- message("No. of particles: [%d, %d]", global_nr_gparts[0], global_nr_gparts[1]);
+ printf("No. of particles: [%d", global_nr_gparts[0]);
+ for(int i = 1; i<s->e->nr_nodes; i++) printf(", %d", global_nr_gparts[i]);
+ printf("]\n");
for(int i = 0; i<engine_rank; i++) node_offset += global_nr_gparts[i];
}
@@ -1418,7 +1333,13 @@ void fof_search_tree(struct space *s) {
bzero(global_group_size, s->e->total_nr_gparts * sizeof(int));
bzero(global_group_id, s->e->total_nr_gparts * sizeof(long long));
- int displ[2] = {0, nr_gparts};
+ int *displ = NULL;
+ if (posix_memalign((void**)&displ, SWIFT_STRUCT_ALIGNMENT,
+ s->e->nr_nodes * sizeof(int)) != 0)
+ error("Error while allocating memory for FOF MPI communication");
+
+ displ[0] = 0;
+ for(int i=1; i<s->e->nr_nodes; i++) displ[i] = displ[i-1] + global_nr_gparts[i-1];
MPI_Gatherv(group_index, nr_gparts, MPI_INT, global_group_index, global_nr_gparts, displ, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Gatherv(group_id, nr_gparts, MPI_LONG_LONG, global_group_id, global_nr_gparts, displ, MPI_LONG_LONG, 0, MPI_COMM_WORLD);
diff --git a/src/fof.h b/src/fof.h
index 2d748bfd6cb17d1cf23a723b0d4c5c694caa33ba..50d1edaf0ca171d999df4a1608a4fd719e82e2aa 100644
--- a/src/fof.h
+++ b/src/fof.h
@@ -47,7 +47,6 @@ void fof_search_serial(struct space *s);
void fof_search_cell(struct space *s, struct cell *c);
void fof_search_pair_cells(struct space *s, struct cell *ci, struct cell *cj);
void fof_search_pair_cells_foreign(struct space *s, struct cell *ci, struct cell *cj, size_t *send_count, struct fof_mpi *fof_send);
-void fof_search_pair_cells_foreign_new(struct space *s, struct cell *ci, struct cell *cj, size_t *send_count, struct fof_mpi *fof_send);
void fof_search_tree_serial(struct space *s);
void fof_search_tree(struct space *s);
void fof_dump_group_data(char *out_file, const size_t nr_gparts, int *group_index, int *num_in_groups, long long *group_id);