Skip to content
GitLab
Commit b0e4a2a0 authored by Peter W. Draper's avatar Peter W. Draper
Browse files

Move all repartitioning code out of engine and into partition

parent 24db049f
Hide whitespace changes
Inline Side-by-side
src/engine.c
View file @ b0e4a2a0
......@@ -34,10 +34,6 @@
/* MPI headers. */
#ifdef WITH_MPI
#include <mpi.h>
/* METIS headers only used when MPI is also available. */
#ifdef HAVE_METIS
#include <metis.h>
#endif
#endif
#ifdef HAVE_LIBNUMA
......@@ -287,354 +283,6 @@ void engine_redistribute(struct engine *e) {
#endif
}
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Accumulate the counts of particles per cell.
*
* @param s the space containing the cells.
* @param counts the number of particles per cell. Should be
* allocated as size s->nr_parts.
*/
static void metis_repart_counts(struct space *s, int *counts) {
struct part *parts = s->parts;
int *cdim = s->cdim;
double ih[3], dim[3];
ih[0] = s->ih[0];
ih[1] = s->ih[1];
ih[2] = s->ih[2];
dim[0] = s->dim[0];
dim[1] = s->dim[1];
dim[2] = s->dim[2];
bzero(counts, sizeof(int) * s->nr_cells);
for (int k = 0; k < s->nr_parts; k++) {
for (int j = 0; j < 3; j++) {
if (parts[k].x[j] < 0.0)
parts[k].x[j] += dim[j];
else if (parts[k].x[j] >= dim[j])
parts[k].x[j] -= dim[j];
}
const int cid = cell_getid(cdim, parts[k].x[0] * ih[0],
parts[k].x[1] * ih[1], parts[k].x[2] * ih[2]);
counts[cid]++;
}
}
#endif
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Repartition the cells amongst the nodes using task timings
* as edge weights and vertex weights also from task timings
* or particle cells counts.
*
* @param partweights whether particle counts will be used as vertex weights.
* @param bothweights whether vertex and edge weights will be used, otherwise
* only edge weights will be used.
* @param e The #engine.
*/
static void metis_repart_edge(int partweights, int bothweights, struct engine *e) {
/* Create weight arrays using task ticks for vertices and edges (edges
* assume the same graph structure as used in the part_ calls). */
int nr_nodes = e->nr_nodes;
int nodeID = e->nodeID;
struct space *s = e->s;
int nr_cells = s->nr_cells;
struct cell *cells = s->cells;
struct task *tasks = e->sched.tasks;
float wscale = 1e-3, vscale = 1e-3, wscale_buff;
int wtot = 0;
int wmax = 1e9 / nr_nodes;
int wmin;
/* Allocate and fill the adjncy indexing array defining the graph of
* cells. */
idx_t *inds;
if ((inds = (idx_t *)malloc(sizeof(idx_t) * 26 * nr_cells)) == NULL)
error("Failed to allocate the inds array");
part_graph_init_metis(s, inds, NULL);
/* Allocate and init weights. */
int *weights_v = NULL;
int *weights_e = NULL;
if (bothweights) {
if ((weights_v = (int *)malloc(sizeof(int) * nr_cells)) == NULL)
error("Failed to allocate vertex weights arrays.");
bzero(weights_v, sizeof(int) * nr_cells);
}
if ((weights_e = (int *)malloc(sizeof(int) * 26 * nr_cells)) == NULL)
error("Failed to allocate edge weights arrays.");
bzero(weights_e, sizeof(int) * 26 * nr_cells);
/* Generate task weights for vertices. */
int taskvweights = (bothweights && !partweights);
/* Loop over the tasks... */
for (int j = 0; j < e->sched.nr_tasks; j++) {
/* Get a pointer to the kth task. */
struct task *t = &tasks[j];
/* Skip un-interesting tasks. */
if (t->type != task_type_self && t->type != task_type_pair &&
t->type != task_type_sub && t->type != task_type_ghost &&
t->type != task_type_drift && t->type != task_type_kick &&
t->type != task_type_init)
continue;
/* Get the task weight. */
int w = (t->toc - t->tic) * wscale;
if (w < 0) error("Bad task weight (%d).", w);
/* Do we need to re-scale? */
wtot += w;
while (wtot > wmax) {
wscale /= 2;
wtot /= 2;
w /= 2;
for (int k = 0; k < 26 * nr_cells; k++) weights_e[k] *= 0.5;
if (taskvweights)
for (int k = 0; k < nr_cells; k++) weights_v[k] *= 0.5;
}
/* Get the top-level cells involved. */
struct cell *ci, *cj;
for (ci = t->ci; ci->parent != NULL; ci = ci->parent)
;
if (t->cj != NULL)
for (cj = t->cj; cj->parent != NULL; cj = cj->parent)
;
else
cj = NULL;
/* Get the cell IDs. */
int cid = ci - cells;
/* Different weights for different tasks. */
if (t->type == task_type_ghost || t->type == task_type_drift ||
t->type == task_type_kick) {
/* Particle updates add only to vertex weight. */
if (taskvweights)
weights_v[cid] += w;
}
/* Self interaction? */
else if ((t->type == task_type_self && ci->nodeID == nodeID) ||
(t->type == task_type_sub && cj == NULL &&
ci->nodeID == nodeID)) {
/* Self interactions add only to vertex weight. */
if (taskvweights)
weights_v[cid] += w;
}
/* Pair? */
else if (t->type == task_type_pair ||
(t->type == task_type_sub && cj != NULL)) {
/* In-cell pair? */
if (ci == cj) {
/* Add weight to vertex for ci. */
if (taskvweights)
weights_v[cid] += w;
}
/* Distinct cells with local ci? */
else if (ci->nodeID == nodeID) {
/* Index of the jth cell. */
int cjd = cj - cells;
/* Add half of weight to each cell. */
if (taskvweights) {
if (ci->nodeID == nodeID) weights_v[cid] += 0.5 * w;
if (cj->nodeID == nodeID) weights_v[cjd] += 0.5 * w;
}
/* Add weights to edge. */
int kk;
for (kk = 26 * cid; inds[kk] != cjd; kk++)
;
weights_e[kk] += w;
for (kk = 26 * cjd; inds[kk] != cid; kk++)
;
weights_e[kk] += w;
}
}
}
/* Re-calculate the vertices if using particle counts. */
if (partweights && bothweights) {
metis_repart_counts(s, weights_v);
/* Rescale to balance times. */
float vwscale = (float)wtot / (float)e->sched.nr_tasks;
for (int k = 0; k < nr_cells; k++) {
weights_v[k] *= vwscale;
}
}
/* Get the minimum scaling and re-scale if necessary. */
int res;
if ((res = MPI_Allreduce(&wscale, &wscale_buff, 1, MPI_FLOAT, MPI_MIN,
MPI_COMM_WORLD)) != MPI_SUCCESS)
mpi_error(res, "Failed to allreduce the weight scales.");
if (wscale_buff != wscale) {
float scale = wscale_buff / wscale;
for (int k = 0; k < 26 * nr_cells; k++) weights_e[k] *= scale;
if (bothweights)
for (int k = 0; k < nr_cells; k++) weights_v[k] *= scale;
}
/* Merge the weights arrays across all nodes. */
if (bothweights) {
if ((res = MPI_Reduce((nodeID == 0) ? MPI_IN_PLACE : weights_v, weights_v,
nr_cells, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD)) !=
MPI_SUCCESS)
mpi_error(res, "Failed to allreduce vertex weights.");
}
if ((res = MPI_Reduce((nodeID == 0) ? MPI_IN_PLACE : weights_e, weights_e,
26 * nr_cells, MPI_INT, MPI_SUM, 0,
MPI_COMM_WORLD)) != MPI_SUCCESS)
mpi_error(res, "Failed to allreduce edge weights.");
/* Allocate cell list for the partition. */
int *celllist = (int *)malloc(sizeof(int) * s->nr_cells);
if (celllist == NULL) error("Failed to allocate celllist");
/* As of here, only one node needs to compute the partition. */
if (nodeID == 0) {
/* Final rescale of all weights to avoid a large range. Large ranges
* have been seen to cause an incomplete graph. */
wmin = wmax;
wmax = 0;
for (int k = 0; k < 26 * nr_cells; k++) {
wmax = weights_e[k] > wmax ? weights_e[k] : wmax;
wmin = weights_e[k] < wmin ? weights_e[k] : wmin;
}
if (bothweights) {
for (int k = 0; k < nr_cells; k++) {
wmax = weights_v[k] > wmax ? weights_v[k] : wmax;
wmin = weights_v[k] < wmin ? weights_v[k] : wmin;
}
}
if ((wmax - wmin) > engine_maxmetisweight) {
wscale = engine_maxmetisweight / (wmax - wmin);
for (int k = 0; k < 26 * nr_cells; k++) {
weights_e[k] = (weights_e[k] - wmin) * wscale + 1;
}
if (bothweights) {
for (int k = 0; k < nr_cells; k++) {
weights_v[k] = (weights_v[k] - wmin) * wscale + 1;
}
}
}
/* Make sure there are no zero weights. */
for (int k = 0; k < 26 * nr_cells; k++)
if (weights_e[k] == 0) weights_e[k] = 1;
if (bothweights)
for (int k = 0; k < nr_cells; k++)
if ((weights_v[k] *= vscale) == 0) weights_v[k] = 1;
/* And partition, use both weights or not as requested. */
if (bothweights)
part_pick_metis(s, nr_nodes, weights_v, weights_e, celllist);
else
part_pick_metis(s, nr_nodes, NULL, weights_e, celllist);
/* Check that all cells have good values. */
for (int k = 0; k < nr_cells; k++)
if (celllist[k] < 0 || celllist[k] >= nr_nodes)
error("Got bad nodeID %d for cell %i.", celllist[k], k);
/* Check that the partition is complete and all nodes have some work. */
int present[nr_nodes];
int failed = 0;
for (int i = 0; i < nr_nodes; i++) present[i] = 0;
for (int i = 0; i < nr_cells; i++) present[celllist[i]]++;
for (int i = 0; i < nr_nodes; i++) {
if (!present[i]) {
failed = 1;
message("Node %d is not present after repartition", i);
}
}
/* If partition failed continue with the current one, but make this
* clear. */
if (failed) {
message(
"WARNING: METIS repartition has failed, continuing with "
"the current partition, load balance will not be optimal");
for (int k = 0; k < nr_cells; k++) celllist[k] = cells[k].nodeID;
}
}
/* Distribute the celllist partition and apply. */
if ((res = MPI_Bcast(celllist, s->nr_cells, MPI_INT, 0, MPI_COMM_WORLD)) !=
MPI_SUCCESS)
mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
part_split_metis(s, nr_nodes, celllist);
/* Clean up. */
if (bothweights) free(weights_v);
free(weights_e);
free(celllist);
}
#endif
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Repartition the cells amongst the nodes using vertex weights
*
* @param e The #engine.
*/
static void metis_repart_vertex(struct engine *e) {
struct space *s = e->s;
/* Use particle counts as vertex weights. */
/* Space for particles per cell counts, which will be used as weights. */
int *weights = NULL;
if ((weights = (int *)malloc(sizeof(int) * s->nr_cells)) == NULL)
error("Failed to allocate weights buffer.");
/* Check each particle and accumulate the counts per cell. */
metis_repart_counts(s, weights);
/* Get all the counts from all the nodes. */
int res;
if ((res = MPI_Allreduce(MPI_IN_PLACE, weights, s->nr_cells, MPI_INT,
MPI_SUM, MPI_COMM_WORLD)) != MPI_SUCCESS)
mpi_error(res, "Failed to allreduce particle cell weights.");
/* Main node does the partition calculation. */
int *celllist = (int *)malloc(sizeof(int) * s->nr_cells);
if (celllist == NULL) error("Failed to allocate celllist");
if (e->nodeID == 0)
part_pick_metis(s, e->nr_nodes, weights, NULL, celllist);
/* Distribute the celllist partition and apply. */
if ((res = MPI_Bcast(celllist, s->nr_cells, MPI_INT, 0, MPI_COMM_WORLD)) !=
MPI_SUCCESS)
mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
part_split_metis(s, e->nr_nodes, celllist);
free(weights);
free(celllist);
}
#endif
/**
* @brief Repartition the cells amongst the nodes.
......@@ -655,15 +303,8 @@ void engine_repartition(struct engine *e) {
if (e->nr_nodes == 1) return;
/* Do the repartitioning. */
if (reparttype == REPART_METIS_BOTH || reparttype == REPART_METIS_EDGE ||
reparttype == REPART_METIS_VERTEX_EDGE) {
metis_repart_edge(reparttype == REPART_METIS_VERTEX_EDGE,
reparttype == REPART_METIS_BOTH, e);
} else if (reparttype == REPART_METIS_VERTEX) {
metis_repart_vertex(e);
}
part_repart(reparttype, e->nodeID, e->nr_nodes, e->s, e->sched.tasks,
e->sched.nr_tasks);
/* Now comes the tricky part: Exchange particles between all nodes.
This is done in two steps, first allreducing a matrix of
......
src/engine.h
View file @ b0e4a2a0
......@@ -63,7 +63,6 @@ extern const char *engine_policy_names[];
#define engine_maxproxies 64
#define engine_tasksreweight 10
#define engine_maxmetisweight 10000.0f
/* The rank of the engine as a global variable (for messages). */
extern int engine_rank;
......
src/partition.c
View file @ b0e4a2a0
......@@ -33,6 +33,7 @@
#include <stdlib.h>
#include <math.h>
#include <values.h>
#include <strings.h>
/* MPI headers. */
#ifdef WITH_MPI
......@@ -55,17 +56,20 @@
#define MIN(a, b) ((a) > (b) ? (b) : (a))
#define CHUNK 512
/* Maximum weight used for METIS. */
#define metis_maxweight 10000.0f
/* Simple descriptions of initial partition types for reports. */
const char *initpart_name[] = {
"gridded cells",
"vectorized point associated cells",
"METIS particle weighted cells",
"METIS particle weighted cells",
"METIS unweighted cells"
};
/* Simple descriptions of repartition types for reports. */
const char *repart_name[] = {
"no",
"no",
"METIS edge and vertex time weighted cells",
"METIS particle count vertex weighted cells",
"METIS time edge weighted cells",
......@@ -154,7 +158,7 @@ void part_split_vector(struct space *s, int nregions, int *samplecells) {
* weighted by the number of particles scheme. Note METIS is optional.
*/
/**
/**
* @brief Fill the METIS xadj and adjncy arrays defining the graph of cells
* in a space.
*
......@@ -168,8 +172,8 @@ void part_split_vector(struct space *s, int nregions, int *samplecells) {
* @param xadj the METIS xadj array to fill, must be of size
* number of cells in space + 1. NULL for not used.
*/
#ifdef HAVE_METIS
void part_graph_init_metis(struct space *s, idx_t *adjncy, idx_t *xadj) {
#if defined(WITH_MPI) && defined(HAVE_METIS)
static void graph_init_metis(struct space *s, idx_t *adjncy, idx_t *xadj) {
/* Loop over all cells in the space. */
int cid = 0;
......@@ -222,6 +226,401 @@ void part_graph_init_metis(struct space *s, idx_t *adjncy, idx_t *xadj) {
}
#endif
/**
* @brief Accumulate the counts of particles per cell.
*
* @param s the space containing the cells.
* @param counts the number of particles per cell. Should be
* allocated as size s->nr_parts.
*/
#if defined(WITH_MPI) && defined(HAVE_METIS)
static void accumulate_counts(struct space *s, int *counts) {
struct part *parts = s->parts;
int *cdim = s->cdim;
double ih[3], dim[3];
ih[0] = s->ih[0];
ih[1] = s->ih[1];
ih[2] = s->ih[2];
dim[0] = s->dim[0];
dim[1] = s->dim[1];
dim[2] = s->dim[2];
bzero(counts, sizeof(int) * s->nr_cells);
for (int k = 0; k < s->nr_parts; k++) {
for (int j = 0; j < 3; j++) {
if (parts[k].x[j] < 0.0)
parts[k].x[j] += dim[j];
else if (parts[k].x[j] >= dim[j])
parts[k].x[j] -= dim[j];
}
const int cid = cell_getid(cdim, parts[k].x[0] * ih[0],
parts[k].x[1] * ih[1], parts[k].x[2] * ih[2]);
counts[cid]++;
}
}
#endif
/**
* @brief Repartition the cells amongst the nodes using task timings
* as edge weights and vertex weights also from task timings
* or particle cells counts.
*
* @param partweights whether particle counts will be used as vertex weights.
* @param bothweights whether vertex and edge weights will be used, otherwise
* only edge weights will be used.
* @param e The #engine.
*/
#if defined(WITH_MPI) && defined(HAVE_METIS)
static void repart_edge_metis(int partweights, int bothweights,
int nodeID, int nr_nodes, struct space *s,
struct task *tasks, int nr_tasks) {
/* Create weight arrays using task ticks for vertices and edges (edges
* assume the same graph structure as used in the part_ calls). */
int nr_cells = s->nr_cells;
struct cell *cells = s->cells;
float wscale = 1e-3, vscale = 1e-3, wscale_buff;
int wtot = 0;
int wmax = 1e9 / nr_nodes;
int wmin;
/* Allocate and fill the adjncy indexing array defining the graph of
* cells. */
idx_t *inds;
if ((inds = (idx_t *)malloc(sizeof(idx_t) * 26 * nr_cells)) == NULL)
error("Failed to allocate the inds array");
graph_init_metis(s, inds, NULL);
/* Allocate and init weights. */
int *weights_v = NULL;
int *weights_e = NULL;
if (bothweights) {
if ((weights_v = (int *)malloc(sizeof(int) * nr_cells)) == NULL)
error("Failed to allocate vertex weights arrays.");
bzero(weights_v, sizeof(int) * nr_cells);
}
if ((weights_e = (int *)malloc(sizeof(int) * 26 * nr_cells)) == NULL)
error("Failed to allocate edge weights arrays.");
bzero(weights_e, sizeof(int) * 26 * nr_cells);
/* Generate task weights for vertices. */
int taskvweights = (bothweights && !partweights);
/* Loop over the tasks... */
for (int j = 0; j < nr_tasks; j++) {
/* Get a pointer to the kth task. */
struct task *t = &tasks[j];
/* Skip un-interesting tasks. */
if (t->type != task_type_self && t->type != task_type_pair &&
t->type != task_type_sub && t->type != task_type_ghost &&
t->type != task_type_drift && t->type != task_type_kick &&
t->type != task_type_init)
continue;
/* Get the task weight. */
int w = (t->toc - t->tic) * wscale;
if (w < 0) error("Bad task weight (%d).", w);
/* Do we need to re-scale? */
wtot += w;
while (wtot > wmax) {
wscale /= 2;
wtot /= 2;
w /= 2;
for (int k = 0; k < 26 * nr_cells; k++) weights_e[k] *= 0.5;
if (taskvweights)
for (int k = 0; k < nr_cells; k++) weights_v[k] *= 0.5;
}
/* Get the top-level cells involved. */
struct cell *ci, *cj;
for (ci = t->ci; ci->parent != NULL; ci = ci->parent)
;
if (t->cj != NULL)
for (cj = t->cj; cj->parent != NULL; cj = cj->parent)
;
else
cj = NULL;
/* Get the cell IDs. */
int cid = ci - cells;
/* Different weights for different tasks. */
if (t->type == task_type_ghost || t->type == task_type_drift ||
t->type == task_type_kick) {
/* Particle updates add only to vertex weight. */
if (taskvweights)
weights_v[cid] += w;
}
/* Self interaction? */
else if ((t->type == task_type_self && ci->nodeID == nodeID) ||
(t->type == task_type_sub && cj == NULL &&
ci->nodeID == nodeID)) {
/* Self interactions add only to vertex weight. */
if (taskvweights)
weights_v[cid] += w;
}
/* Pair? */
else if (t->type == task_type_pair ||
(t->type == task_type_sub && cj != NULL)) {
/* In-cell pair? */
if (ci == cj) {
/* Add weight to vertex for ci. */
if (taskvweights)
weights_v[cid] += w;
}
/* Distinct cells with local ci? */
else if (ci->nodeID == nodeID) {
/* Index of the jth cell. */
int cjd = cj - cells;
/* Add half of weight to each cell. */
if (taskvweights) {
if (ci->nodeID == nodeID) weights_v[cid] += 0.5 * w;
if (cj->nodeID == nodeID) weights_v[cjd] += 0.5 * w;
}
/* Add weights to edge. */
int kk;
for (kk = 26 * cid; inds[kk] != cjd; kk++)
;
weights_e[kk] += w;
for (kk = 26 * cjd; inds[kk] != cid; kk++)
;
weights_e[kk] += w;
}