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Commit 0666afd8 authored by Peter W. Draper's avatar Peter W. Draper
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Move initial partition code out of engine and into partition 

Also reduce public partition functions to a simple few
parent 38e72a9c
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src/engine.c
View file @ 0666afd8
......@@ -1730,125 +1730,10 @@ void engine_makeproxies(struct engine *e) {
void engine_split(struct engine *e, struct initpart *ipart) {
#ifdef WITH_MPI
struct space *s = e->s;
if (ipart->type == INITPART_GRID) {
int j, k;
int ind[3];
struct cell *c;
/* If we've got the wrong number of nodes, fail. */
if (e->nr_nodes != ipart->grid[0] * ipart->grid[1] * ipart->grid[2])
error("Grid size does not match number of nodes.");
/* Run through the cells and set their nodeID. */
// message("s->dim = [%e,%e,%e]", s->dim[0], s->dim[1], s->dim[2]);
for (k = 0; k < s->nr_cells; k++) {
c = &s->cells[k];
for (j = 0; j < 3; j++) ind[j] = c->loc[j] / s->dim[j] * ipart->grid[j];
c->nodeID = ind[0] + ipart->grid[0] * (ind[1] + ipart->grid[1] * ind[2]);
// message("cell at [%e,%e,%e]: ind = [%i,%i,%i], nodeID = %i", c->loc[0],
// c->loc[1], c->loc[2], ind[0], ind[1], ind[2], c->nodeID);
}
/* The grid technique can fail, so check for this before proceeding. */
if (!part_check_complete(s, (e->nodeID == 0), e->nr_nodes)) {
if (e->nodeID == 0)
message("Grid initial partition failed, using a vectorised partition");
ipart->type = INITPART_VECTORIZE;
engine_split(e, ipart);
return;
}
} else if (ipart->type == INITPART_METIS_WEIGHT ||
ipart->type == INITPART_METIS_NOWEIGHT) {
/* Simple k-way partition selected by METIS using cell particle counts as
* weights or not. Should be best when starting with a inhomogeneous dist.
*/
/* Space for particles per cell counts, which will be used as weights or
* not. */
int *weights = NULL;
if (ipart->type == INITPART_METIS_WEIGHT) {
if ((weights = (int *)malloc(sizeof(int) * s->nr_cells)) == NULL)
error("Failed to allocate weights buffer.");
bzero(weights, sizeof(int) * s->nr_cells);
/* Check each particle and accumilate the counts per cell. */
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];
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]);
weights[cid]++;
}
/* Get all the counts from all the nodes. */
if (MPI_Allreduce(MPI_IN_PLACE, weights, s->nr_cells, MPI_INT, MPI_SUM,
MPI_COMM_WORLD) != MPI_SUCCESS)
error("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. */
int res = MPI_Bcast(celllist, s->nr_cells, MPI_INT, 0, MPI_COMM_WORLD);
if (res != MPI_SUCCESS) mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
part_split_metis(s, e->nr_nodes, celllist);
/* It's not known if this can fail, but check for this before proceeding. */
if (!part_check_complete(s, (e->nodeID == 0), e->nr_nodes)) {
if (e->nodeID == 0)
message("METIS initial partition failed, using a vectorised partition");
ipart->type = INITPART_VECTORIZE;
engine_split(e, ipart);
}
if (weights != NULL) free(weights);
free(celllist);
} else if (ipart->type == INITPART_VECTORIZE) {
/* Vectorised selection, guaranteed to work for samples less than the
* number of cells, but not very clumpy in the selection of regions. */
int *samplecells = (int *)malloc(sizeof(int) * e->nr_nodes * 3);
if (samplecells == NULL) error("Failed to allocate samplecells");
if (e->nodeID == 0) {
part_pick_vector(s, e->nr_nodes, samplecells);
}
/* Share the samplecells around all the nodes. */
int res =
MPI_Bcast(samplecells, e->nr_nodes * 3, MPI_INT, 0, MPI_COMM_WORLD);
if (res != MPI_SUCCESS)
mpi_error(res, "Failed to bcast the partition sample cells.");
/* And apply to our cells */
part_split_vector(s, e->nr_nodes, samplecells);
free(samplecells);
}
/* Do the initial partition of the cells. */
part_part(ipart, e->nodeID, e->nr_nodes, s);
/* Make the proxies. */
engine_makeproxies(e);
......
src/partition.c
View file @ 0666afd8
......@@ -19,7 +19,7 @@
/**
* @file partition.c
* @brief file of various techniques for partitioning and repartitioning
* @brief file of various techniques for partitioning and repartitioning
* a grid of cells into geometrically connected regions.
*
* Currently supported types, grid, vectorise and METIS.
......@@ -79,6 +79,7 @@ const char *repart_name[] = {
/* Vectorisation support */
/* ===================== */
#if defined(WITH_MPI)
/**
* @brief Pick a number of cell positions from a vectorised list.
*
......@@ -90,7 +91,7 @@ const char *repart_name[] = {
* @param nregions the number of regions
* @param samplecells the list of sample cell positions, size of 3*nregions
*/
void part_pick_vector(struct space *s, int nregions, int *samplecells) {
static void pick_vector(struct space *s, int nregions, int *samplecells) {
/* Get length of space and divide up. */
int length = s->cdim[0] * s->cdim[1] * s->cdim[2];
......@@ -119,14 +120,16 @@ void part_pick_vector(struct space *s, int nregions, int *samplecells) {
}
}
}
#endif
#if defined(WITH_MPI)
/**
* @brief Partition the space.
*
* Using the sample positions as seeds pick cells that are geometry closest
* to each and apply the partition to the space.
*/
void part_split_vector(struct space *s, int nregions, int *samplecells) {
static void split_vector(struct space *s, int nregions, int *samplecells) {
int n = 0;
for (int i = 0; i < s->cdim[0]; i++) {
for (int j = 0; j < s->cdim[1]; j++) {
......@@ -149,6 +152,7 @@ void part_split_vector(struct space *s, int nregions, int *samplecells) {
}
}
}
#endif
/* METIS support
* =============
......@@ -262,6 +266,143 @@ static void accumulate_counts(struct space *s, int *counts) {
}
#endif
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Apply METIS cell list partitioning to a cell structure.
*
* Uses the results of part_metis_pick to assign each cell's nodeID to the
* picked region index, thus partitioning the space into regions.
*
* @param s the space containing the cells to split into regions.
* @param nregions number of regions.
* @param celllist list of regions for each cell.
*/
static void split_metis(struct space *s, int nregions, int *celllist) {
for (int i = 0; i < s->nr_cells; i++)
s->cells[i].nodeID = celllist[i];
}
#endif
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Partition the given space into a number of connected regions.
*
* Split the space using METIS to derive a partitions using the
* cell particle counts as weights.
*
* @param s the space of cells to partition.
* @param nregions the number of regions required in the partition.
* @param vertexw weights for the cells, sizeof number of cells if used,
* NULL for unit weights.
* @param edgew weights for the graph edges between all cells, sizeof number
* of cells * 26 if used, NULL for unit weights. Need to be packed
* in CSR format, so same as adjncy array.
* @param celllist on exit this contains the ids of the selected regions,
* sizeof number of cells.
*/
static void pick_metis(struct space *s, int nregions, int *vertexw, int *edgew,
int *celllist) {
/* Total number of cells. */
int ncells = s->cdim[0] * s->cdim[1] * s->cdim[2];
/* Nothing much to do if only using a single partition. Also avoids METIS
* bug that doesn't handle this case well. */
if (nregions == 1) {
for (int i = 0; i < ncells; i++) celllist[i] = 0;
return;
}
/* Allocate weights and adjacency arrays . */
idx_t *xadj;
if ((xadj = (idx_t *)malloc(sizeof(idx_t) * (ncells + 1))) == NULL)
error("Failed to allocate xadj buffer.");
idx_t *adjncy;
if ((adjncy = (idx_t *)malloc(sizeof(idx_t) * 26 * ncells)) == NULL)
error("Failed to allocate adjncy array.");
idx_t *weights_v = NULL;
if (vertexw != NULL)
if ((weights_v = (idx_t *)malloc(sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate vertex weights array");
idx_t *weights_e = NULL;
if (edgew != NULL)
if ((weights_e = (idx_t *)malloc(26 * sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate edge weights array");
idx_t *regionid;
if ((regionid = (idx_t *)malloc(sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate regionid array");
/* Define the cell graph. */
graph_init_metis(s, adjncy, xadj);
/* Init the vertex weights array. */
if (vertexw != NULL) {
for (int k = 0; k < ncells; k++) {
if (vertexw[k] > 0) {
weights_v[k] = vertexw[k];
} else {
weights_v[k] = 1;
}
}
}
/* Init the edges weights array. */
if (edgew != NULL) {
for (int k = 0; k < 26 * ncells; k++) {
if (edgew[k] > 0) {
weights_e[k] = edgew[k];
} else {
weights_e[k] = 1;
}
}
}
/* Set the METIS options. */
idx_t options[METIS_NOPTIONS];
METIS_SetDefaultOptions(options);
options[METIS_OPTION_OBJTYPE] = METIS_OBJTYPE_CUT;
options[METIS_OPTION_NUMBERING] = 0;
options[METIS_OPTION_CONTIG] = 1;
options[METIS_OPTION_NCUTS] = 10;
options[METIS_OPTION_NITER] = 20;
/* Call METIS. */
idx_t one = 1;
idx_t idx_ncells = ncells;
idx_t idx_nregions = nregions;
idx_t objval;
/* Dump graph in METIS format */
/* dumpMETISGraph("metis_graph", idx_ncells, one, xadj, adjncy,
* weights_v, weights_e, NULL);
*/
if (METIS_PartGraphKway(&idx_ncells, &one, xadj, adjncy, weights_v, weights_e,
NULL, &idx_nregions, NULL, NULL, options, &objval,
regionid) != METIS_OK)
error("Call to METIS_PartGraphKway failed.");
/* Check that the regionids are ok. */
for (int k = 0; k < ncells; k++)
if (regionid[k] < 0 || regionid[k] >= nregions)
error("Got bad nodeID %" PRIDX " for cell %i.", regionid[k], k);
/* Set the cell list to the region index. */
for (int k = 0; k < ncells; k++) {
celllist[k] = regionid[k];
}
/* Clean up. */
if (weights_v != NULL) free(weights_v);
if (weights_e != NULL) free(weights_e);
free(xadj);
free(adjncy);
free(regionid);
}
#endif
#if defined(WITH_MPI) && defined(HAVE_METIS)
/**
* @brief Repartition the cells amongst the nodes using task timings
......@@ -485,9 +626,9 @@ static void repart_edge_metis(int partweights, int bothweights,
/* And partition, use both weights or not as requested. */
if (bothweights)
part_pick_metis(s, nr_nodes, weights_v, weights_e, celllist);
pick_metis(s, nr_nodes, weights_v, weights_e, celllist);
else
part_pick_metis(s, nr_nodes, NULL, weights_e, celllist);
pick_metis(s, nr_nodes, NULL, weights_e, celllist);
/* Check that all cells have good values. */
for (int k = 0; k < nr_cells; k++)
......@@ -522,7 +663,7 @@ static void repart_edge_metis(int partweights, int bothweights,
mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
part_split_metis(s, nr_nodes, celllist);
split_metis(s, nr_nodes, celllist);
/* Clean up. */
if (bothweights) free(weights_v);
......@@ -561,7 +702,7 @@ static void repart_vertex_metis(struct space *s, int nodeID, int nr_nodes) {
if (celllist == NULL) error("Failed to allocate celllist");
if (nodeID == 0)
part_pick_metis(s, nr_nodes, weights, NULL, celllist);
pick_metis(s, 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)) !=
......@@ -569,13 +710,14 @@ static void repart_vertex_metis(struct space *s, int nodeID, int nr_nodes) {
mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
part_split_metis(s, nr_nodes, celllist);
split_metis(s, nr_nodes, celllist);
free(weights);
free(celllist);
}
#endif
/**
* @brief Repartition the space using the given repartition type.
*
......@@ -624,142 +766,151 @@ void part_repart(enum repart_type reparttype, int nodeID, int nr_nodes,
#endif
}
/**
* @brief Partition the given space into a number of connected regions.
* @brief Partition the cells of a space.
*
* Split the space using METIS to derive a partitions using the
* cell particle counts as weights.
* Cells are assigned to a node on the basis of various schemes, all of which
* should attempt to distribute them in geometrically close regions to
* minimise the movement of particles.
*
* @param s the space of cells to partition.
* @param nregions the number of regions required in the partition.
* @param vertexw weights for the cells, sizeof number of cells if used,
* NULL for unit weights.
* @param edgew weights for the graph edges between all cells, sizeof number
* of cells * 26 if used, NULL for unit weights. Need to be packed
* in CSR format, so same as adjncy array.
* @param celllist on exit this contains the ids of the selected regions,
* sizeof number of cells.
* Note that the partition type is a suggestion and will be ignored if that
* scheme fails. In that case we fallback to a vectorised scheme, that is
* guaranteed to work provided we have more cells than nodes.
*
* @param ipart the type of partitioning to try.
* @param nodeID our nodeID.
* @param nr_nodes the number of nodes.
* @param s the space of cells.
*/
void part_pick_metis(struct space *s, int nregions, int *vertexw, int *edgew,
int *celllist) {
#if defined(WITH_MPI) && defined(HAVE_METIS)
/* Total number of cells. */
int ncells = s->cdim[0] * s->cdim[1] * s->cdim[2];
void part_part(struct initpart *ipart, int nodeID, int nr_nodes,
struct space *s) {
/* Geometric grid partitioning. */
if (ipart->type == INITPART_GRID) {
int j, k;
int ind[3];
struct cell *c;
/* If we've got the wrong number of nodes, fail. */
if (nr_nodes != ipart->grid[0] * ipart->grid[1] * ipart->grid[2])
error("Grid size does not match number of nodes.");
/* Run through the cells and set their nodeID. */
// message("s->dim = [%e,%e,%e]", s->dim[0], s->dim[1], s->dim[2]);
for (k = 0; k < s->nr_cells; k++) {
c = &s->cells[k];
for (j = 0; j < 3; j++) ind[j] = c->loc[j] / s->dim[j] * ipart->grid[j];
c->nodeID = ind[0] + ipart->grid[0] * (ind[1] + ipart->grid[1] * ind[2]);
// message("cell at [%e,%e,%e]: ind = [%i,%i,%i], nodeID = %i", c->loc[0],
// c->loc[1], c->loc[2], ind[0], ind[1], ind[2], c->nodeID);
}
/* Nothing much to do if only using a single partition. Also avoids METIS
* bug that doesn't handle this case well. */
if (nregions == 1) {
for (int i = 0; i < ncells; i++) celllist[i] = 0;
return;
}
/* The grid technique can fail, so check for this before proceeding. */
if (!part_check_complete(s, (nodeID == 0), nr_nodes)) {
if (nodeID == 0)
message("Grid initial partition failed, using a vectorised partition");
ipart->type = INITPART_VECTORIZE;
part_part(ipart, nodeID, nr_nodes, s);
return;
}
/* Allocate weights and adjacency arrays . */
idx_t *xadj;
if ((xadj = (idx_t *)malloc(sizeof(idx_t) * (ncells + 1))) == NULL)
error("Failed to allocate xadj buffer.");
idx_t *adjncy;
if ((adjncy = (idx_t *)malloc(sizeof(idx_t) * 26 * ncells)) == NULL)
error("Failed to allocate adjncy array.");
idx_t *weights_v = NULL;
if (vertexw != NULL)
if ((weights_v = (idx_t *)malloc(sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate vertex weights array");
idx_t *weights_e = NULL;
if (edgew != NULL)
if ((weights_e = (idx_t *)malloc(26 * sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate edge weights array");
idx_t *regionid;
if ((regionid = (idx_t *)malloc(sizeof(idx_t) * ncells)) == NULL)
error("Failed to allocate regionid array");
} else if (ipart->type == INITPART_METIS_WEIGHT ||
ipart->type == INITPART_METIS_NOWEIGHT) {
#if defined(WITH_MPI) && defined(HAVE_METIS)
/* Simple k-way partition selected by METIS using cell particle counts as
* weights or not. Should be best when starting with a inhomogeneous dist.
*/
/* Space for particles per cell counts, which will be used as weights or
* not. */
int *weights = NULL;
if (ipart->type == INITPART_METIS_WEIGHT) {
if ((weights = (int *)malloc(sizeof(int) * s->nr_cells)) == NULL)
error("Failed to allocate weights buffer.");
bzero(weights, sizeof(int) * s->nr_cells);
/* Check each particle and accumilate the counts per cell. */
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];
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]);
weights[cid]++;
}
/* Define the cell graph. */
graph_init_metis(s, adjncy, xadj);
/* Get all the counts from all the nodes. */
if (MPI_Allreduce(MPI_IN_PLACE, weights, s->nr_cells, MPI_INT, MPI_SUM,
MPI_COMM_WORLD) != MPI_SUCCESS)
error("Failed to allreduce particle cell weights.");
/* Init the vertex weights array. */
if (vertexw != NULL) {
for (int k = 0; k < ncells; k++) {
if (vertexw[k] > 0) {
weights_v[k] = vertexw[k];
} else {
weights_v[k] = 1;
}
}
}
/* Init the edges weights array. */
if (edgew != NULL) {
for (int k = 0; k < 26 * ncells; k++) {
if (edgew[k] > 0) {
weights_e[k] = edgew[k];
} else {
weights_e[k] = 1;
}
/* Main node does the partition calculation. */
int *celllist = (int *)malloc(sizeof(int) * s->nr_cells);
if (celllist == NULL) error("Failed to allocate celllist");
if (nodeID == 0)
pick_metis(s, nr_nodes, weights, NULL, celllist);
/* Distribute the celllist partition and apply. */
int res = MPI_Bcast(celllist, s->nr_cells, MPI_INT, 0, MPI_COMM_WORLD);
if (res != MPI_SUCCESS) mpi_error(res, "Failed to bcast the cell list");
/* And apply to our cells */
split_metis(s, nr_nodes, celllist);
/* It's not known if this can fail, but check for this before proceeding. */
if (!part_check_complete(s, (nodeID == 0), nr_nodes)) {
if (nodeID == 0)
message("METIS initial partition failed, using a vectorised partition");
ipart->type = INITPART_VECTORIZE;
part_part(ipart, nodeID, nr_nodes, s);
}
}
/* Set the METIS options. */
idx_t options[METIS_NOPTIONS];
METIS_SetDefaultOptions(options);
options[METIS_OPTION_OBJTYPE] = METIS_OBJTYPE_CUT;
options[METIS_OPTION_NUMBERING] = 0;
options[METIS_OPTION_CONTIG] = 1;
options[METIS_OPTION_NCUTS] = 10;
options[METIS_OPTION_NITER] = 20;
/* Call METIS. */
idx_t one = 1;
idx_t idx_ncells = ncells;
idx_t idx_nregions = nregions;
idx_t objval;
/* Dump graph in METIS format */
/* dumpMETISGraph("metis_graph", idx_ncells, one, xadj, adjncy,
* weights_v, weights_e, NULL);
*/
if (weights != NULL) free(weights);
free(celllist);
#else
error("SWIFT was not compiled with METIS support");
#endif
if (METIS_PartGraphKway(&idx_ncells, &one, xadj, adjncy, weights_v, weights_e,
NULL, &idx_nregions, NULL, NULL, options, &objval,
regionid) != METIS_OK)
error("Call to METIS_PartGraphKway failed.");
} else if (ipart->type == INITPART_VECTORIZE) {
/* Check that the regionids are ok. */
for (int k = 0; k < ncells; k++)
if (regionid[k] < 0 || regionid[k] >= nregions)
error("Got bad nodeID %" PRIDX " for cell %i.", regionid[k], k);
#if defined(WITH_MPI)
/* Vectorised selection, guaranteed to work for samples less than the
* number of cells, but not very clumpy in the selection of regions. */
int *samplecells = (int *)malloc(sizeof(int) * nr_nodes * 3);
if (samplecells == NULL) error("Failed to allocate samplecells");
/* Set the cell list to the region index. */
for (int k = 0; k < ncells; k++) {
celllist[k] = regionid[k];
}
if (nodeID == 0) {
pick_vector(s, nr_nodes, samplecells);
}
/* Clean up. */
if (weights_v != NULL) free(weights_v);
if (weights_e != NULL) free(weights_e);
free(xadj);
free(adjncy);
free(regionid);
/* Share the samplecells around all the nodes. */
int res =
MPI_Bcast(samplecells, nr_nodes * 3, MPI_INT, 0, MPI_COMM_WORLD);
if (res != MPI_SUCCESS)
mpi_error(res, "Failed to bcast the partition sample cells.");
/* And apply to our cells */
split_vector(s, nr_nodes, samplecells);
free(samplecells);
#else
error("SWIFT was not compiled with METIS support.");
error("SWIFT was not compiled with MPI support");
#endif