1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661
|
// Copyright (C) 2019-2020 Garth N. Wells, Chris Richardson and Igor A. Baratta
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier: LGPL-3.0-or-later
#include "partitioners.h"
#include <algorithm>
#include <cstdint>
#include <dolfinx/common/MPI.h>
#include <dolfinx/common/Timer.h>
#include <dolfinx/common/log.h>
#include <map>
#include <numeric>
#include <set>
#include <vector>
#ifdef HAS_PTSCOTCH
extern "C"
{
#include <ptscotch.h>
}
#endif
#ifdef HAS_PARMETIS
extern "C"
{
#include <parmetis.h>
}
#endif
#ifdef HAS_KAHIP
#include <parhip_interface.h>
#endif
using namespace dolfinx;
namespace
{
/// @todo Is it un-documented that the owning rank must come first in
/// reach list of edges?
///
/// @param[in] comm The communicator
/// @param[in] graph Graph, using global indices for graph edges
/// @param[in] node_disp The distribution of graph nodes across MPI
/// ranks. The global index `gidx` of local index `lidx` is `lidx +
/// node_disp[my_rank]`.
/// @param[in] part The destination rank for owned nodes, i.e. `dest[i]`
/// is the destination of the node with local index `i`.
/// @return Destination ranks for each local node.
template <typename T>
graph::AdjacencyList<int> compute_destination_ranks(
MPI_Comm comm, const graph::AdjacencyList<std::int64_t>& graph,
const std::vector<T>& node_disp, const std::vector<T>& part)
{
common::Timer timer("Extend graph destination ranks for halo");
const int rank = dolfinx::MPI::rank(comm);
const std::int64_t range0 = node_disp[rank];
const std::int64_t range1 = node_disp[rank + 1];
assert(static_cast<std::int32_t>(range1 - range0) == graph.num_nodes());
// Wherever an owned 'node' goes, so must the nodes connected to it by
// an edge ('node1'). Task is to let the owner of node1 know the extra
// ranks that it needs to send node1 to.
std::vector<std::array<std::int64_t, 3>> node_to_dest;
for (int node0 = 0; node0 < graph.num_nodes(); ++node0)
{
// Wherever 'node' goes to, so must the attached 'node1'
for (auto node1 : graph.links(node0))
{
if (node1 < range0 or node1 >= range1)
{
auto it = std::ranges::upper_bound(node_disp, node1);
int remote_rank = std::distance(node_disp.begin(), it) - 1;
node_to_dest.push_back(
{remote_rank, node1, static_cast<std::int64_t>(part[node0])});
}
else
node_to_dest.push_back(
{rank, node1, static_cast<std::int64_t>(part[node0])});
}
}
std::ranges::sort(node_to_dest);
auto [unique_end, range_end] = std::ranges::unique(node_to_dest);
node_to_dest.erase(unique_end, range_end);
// Build send data and buffer
std::vector<int> dest, send_sizes;
std::vector<std::int64_t> send_buffer;
{
auto it = node_to_dest.begin();
while (it != node_to_dest.end())
{
// Current destination rank
dest.push_back((*it)[0]);
// Find iterator to next destination rank and pack send data
auto it1
= std::find_if(it, node_to_dest.end(), [r0 = dest.back()](auto& idx)
{ return idx[0] != r0; });
send_sizes.push_back(2 * std::distance(it, it1));
for (auto itx = it; itx != it1; ++itx)
{
send_buffer.push_back((*itx)[1]);
send_buffer.push_back((*itx)[2]);
}
it = it1;
}
}
// Prepare send displacements
std::vector<int> send_disp(send_sizes.size() + 1, 0);
std::partial_sum(send_sizes.begin(), send_sizes.end(),
std::next(send_disp.begin()));
// Discover src ranks. ParMETIS/KaHIP are not scalable (holding an
// array of size equal to the comm size), so no extra harm in using
// non-scalable neighbourhood detection (which might be faster for
// small rank counts).
const std::vector<int> src
= dolfinx::MPI::compute_graph_edges_pcx(comm, dest);
// Create neighbourhood communicator
MPI_Comm neigh_comm;
MPI_Dist_graph_create_adjacent(comm, src.size(), src.data(), MPI_UNWEIGHTED,
dest.size(), dest.data(), MPI_UNWEIGHTED,
MPI_INFO_NULL, false, &neigh_comm);
// Determine receives sizes
std::vector<int> recv_sizes(dest.size());
send_sizes.reserve(1);
recv_sizes.reserve(1);
MPI_Neighbor_alltoall(send_sizes.data(), 1, MPI_INT, recv_sizes.data(), 1,
MPI_INT, neigh_comm);
// Prepare receive displacements
std::vector<int> recv_disp(recv_sizes.size() + 1, 0);
std::partial_sum(recv_sizes.begin(), recv_sizes.end(),
std::next(recv_disp.begin()));
// Send/receive data
std::vector<std::int64_t> recv_buffer(recv_disp.back());
MPI_Neighbor_alltoallv(send_buffer.data(), send_sizes.data(),
send_disp.data(), MPI_INT64_T, recv_buffer.data(),
recv_sizes.data(), recv_disp.data(), MPI_INT64_T,
neigh_comm);
MPI_Comm_free(&neigh_comm);
// Prepare (local node index, destination rank) array. Add local data,
// then add the received data, and the make unique.
std::vector<std::array<int, 2>> local_node_to_dest;
for (auto d : part)
{
local_node_to_dest.push_back(
{static_cast<int>(local_node_to_dest.size()), static_cast<int>(d)});
}
for (std::size_t i = 0; i < recv_buffer.size(); i += 2)
{
std::int64_t idx = recv_buffer[i];
int d = recv_buffer[i + 1];
assert(idx >= range0 and idx < range1);
std::int32_t idx_local = idx - range0;
local_node_to_dest.push_back({idx_local, d});
}
{
std::ranges::sort(local_node_to_dest);
auto [unique_end, range_end] = std::ranges::unique(local_node_to_dest);
local_node_to_dest.erase(unique_end, range_end);
}
// Compute offsets
std::vector<std::int32_t> offsets(graph.num_nodes() + 1, 0);
{
std::vector<std::int32_t> num_dests(graph.num_nodes(), 0);
for (auto x : local_node_to_dest)
++num_dests[x[0]];
std::partial_sum(num_dests.begin(), num_dests.end(),
std::next(offsets.begin()));
}
// Fill data array
std::vector<int> data(offsets.back());
{
std::vector<std::int32_t> pos = offsets;
for (auto [x0, x1] : local_node_to_dest)
data[pos[x0]++] = x1;
}
graph::AdjacencyList<int> g(std::move(data), std::move(offsets));
// Make sure the owning rank comes first for each node
for (std::int32_t i = 0; i < g.num_nodes(); ++i)
{
auto d = g.links(i);
auto it = std::find(d.begin(), d.end(), part[i]);
assert(it != d.end());
std::iter_swap(d.begin(), it);
}
return g;
}
//-----------------------------------------------------------------------------
#ifdef HAS_PARMETIS
template <typename T>
std::vector<int> adaptive_repartition(MPI_Comm comm,
const graph::AdjacencyList<T>& adj_graph,
double weight)
{
common::Timer timer(
"Compute graph partition (ParMETIS Adaptive Repartition)");
// Options for ParMETIS
idx_t options[4];
options[0] = 1;
options[1] = 0;
options[2] = 15;
options[3] = PARMETIS_PSR_UNCOUPLED;
// For repartition, PARMETIS_PSR_COUPLED seems to suppress all
// migration if already balanced. Try PARMETIS_PSR_UNCOUPLED for
// better edge cut.
common::Timer timer1("ParMETIS: call ParMETIS_V3_AdaptiveRepart");
real_t _itr = weight;
std::vector<idx_t> part(adj_graph.num_nodes());
std::vector<idx_t> vsize(part.size(), 1);
assert(!part.empty());
// Number of partitions (one for each process)
idx_t nparts = dolfinx::MPI::size(comm);
// Remaining ParMETIS parameters
idx_t ncon = 1;
idx_t* elmwgt = nullptr;
idx_t wgtflag = 0;
idx_t edgecut = 0;
idx_t numflag = 0;
std::vector<real_t> tpwgts(ncon * nparts, 1.0 / static_cast<real_t>(nparts));
std::vector<real_t> ubvec(ncon, 1.05);
// Call ParMETIS to repartition graph
[[maybe_unused]] int err = ParMETIS_V3_AdaptiveRepart(
adj_graph.node_distribution().data(), adj_graph.nodes().data(),
adj_graph.edges().data(), elmwgt, nullptr, vsize.data(), &wgtflag,
&numflag, &ncon, &nparts, tpwgts.data(), ubvec.data(), &_itr, options,
&edgecut, part.data(), &comm);
assert(err == METIS_OK);
timer1.stop();
// Copy cell partition data and return
return std::vector<int>(part.begin(), part.end());
}
//-----------------------------------------------------------------------------
template <typename T>
std::vector<int> refine(MPI_Comm comm, const graph::AdjacencyList<T>& adj_graph)
{
common::Timer timer("Compute graph partition (ParMETIS Refine)");
// Get some MPI data
const int process_number = dolfinx::MPI::rank(comm);
// Options for ParMETIS
idx_t options[4];
options[0] = 1;
options[1] = 0;
options[2] = 15;
// options[3] = PARMETIS_PSR_UNCOUPLED;
// For repartition, PARMETIS_PSR_COUPLED seems to suppress all
// migration if already balanced. Try PARMETIS_PSR_UNCOUPLED for
// better edge cut.
// Partitioning array to be computed by ParMETIS. Prefill with
// process_number.
const std::int32_t num_local_cells = adj_graph.num_nodes();
std::vector<idx_t> part(num_local_cells, process_number);
assert(!part.empty());
// Number of partitions (one for each process)
idx_t nparts = dolfinx::MPI::size(comm);
// Remaining ParMETIS parameters
idx_t ncon = 1;
idx_t* elmwgt = nullptr;
idx_t wgtflag = 0;
idx_t edgecut = 0;
idx_t numflag = 0;
std::vector<real_t> tpwgts(ncon * nparts, 1.0 / static_cast<real_t>(nparts));
std::vector<real_t> ubvec(ncon, 1.05);
// Call ParMETIS to partition graph
common::Timer timer1("ParMETIS: call ParMETIS_V3_RefineKway");
[[maybe_unused]] int err = ParMETIS_V3_RefineKway(
adj_graph.node_distribution().data(), adj_graph.nodes().data(),
adj_graph.edges().data(), elmwgt, nullptr, &wgtflag, &numflag, &ncon,
&nparts, tpwgts.data(), ubvec.data(), options, &edgecut, part.data(),
&comm);
assert(err == METIS_OK);
timer1.stop();
// Copy cell partition data
return std::vector<int>(part.begin(), part.end());
//-----------------------------------------------------------------------------
}
#endif
} // namespace
//-----------------------------------------------------------------------------
#ifdef HAS_PTSCOTCH
graph::partition_fn graph::scotch::partitioner(graph::scotch::strategy strategy,
double imbalance, int seed)
{
return [imbalance, strategy, seed](MPI_Comm comm, int nparts,
const AdjacencyList<std::int64_t>& graph,
bool ghosting)
{
spdlog::info("Compute graph partition using PT-SCOTCH");
common::Timer timer("Compute graph partition (SCOTCH)");
std::int64_t offset_global = 0;
const std::int64_t num_owned = graph.num_nodes();
MPI_Request request_offset_scan;
MPI_Iexscan(&num_owned, &offset_global, 1, MPI_INT64_T, MPI_SUM, comm,
&request_offset_scan);
// C-style array indexing
constexpr SCOTCH_Num baseval = 0;
// Copy graph data to get the required type (SCOTCH_Num)
std::vector<SCOTCH_Num> edgeloctab(graph.array().begin(),
graph.array().end());
std::vector<SCOTCH_Num> vertloctab(graph.offsets().begin(),
graph.offsets().end());
// Create SCOTCH graph and initialise
SCOTCH_Dgraph dgrafdat;
int err = SCOTCH_dgraphInit(&dgrafdat, comm);
if (err != 0)
throw std::runtime_error("Error initializing SCOTCH graph");
// FIXME: If the nodes have weights but this rank has no nodes, then
// SCOTCH may deadlock since vload.data() will be nullptr on
// this rank but not null on all other ranks.
// Handle node weights (disabled for now)
std::vector<SCOTCH_Num> node_weights;
std::vector<SCOTCH_Num> vload;
if (!node_weights.empty())
vload.assign(node_weights.begin(), node_weights.end());
// Set seed and reset SCOTCH random number generator to produce
// deterministic partitions on repeated calls
SCOTCH_randomSeed(seed);
SCOTCH_randomReset();
// Build SCOTCH distributed graph (SCOTCH is not const-correct, so
// we throw away constness and trust SCOTCH)
common::Timer timer1("SCOTCH: call SCOTCH_dgraphBuild");
err = SCOTCH_dgraphBuild(
&dgrafdat, baseval, graph.num_nodes(), graph.num_nodes(),
vertloctab.data(), nullptr, vload.data(), nullptr, edgeloctab.size(),
edgeloctab.size(), edgeloctab.data(), nullptr, nullptr);
if (err != 0)
throw std::runtime_error("Error building SCOTCH graph");
timer1.stop();
// Check graph data for consistency
#ifndef NDEBUG
err = SCOTCH_dgraphCheck(&dgrafdat);
if (err != 0)
throw std::runtime_error("Consistency error in SCOTCH graph");
#endif
// Initialise partitioning strategy
SCOTCH_Strat strat;
SCOTCH_stratInit(&strat);
// Set SCOTCH strategy
SCOTCH_Num strat_val;
switch (strategy)
{
case strategy::none:
strat_val = SCOTCH_STRATDEFAULT;
break;
case strategy::balance:
strat_val = SCOTCH_STRATBALANCE;
break;
case strategy::quality:
strat_val = SCOTCH_STRATQUALITY;
break;
case strategy::safety:
strat_val = SCOTCH_STRATSAFETY;
break;
case strategy::speed:
strat_val = SCOTCH_STRATSPEED;
break;
case strategy::scalability:
strat_val = SCOTCH_STRATSCALABILITY;
break;
default:
throw std::runtime_error("Unknown SCOTCH strategy");
}
err = SCOTCH_stratDgraphMapBuild(&strat, strat_val, nparts, nparts,
imbalance);
if (err != 0)
throw std::runtime_error("Error calling SCOTCH_stratDgraphMapBuild");
// Count number of 'ghost' edges, i.e. an edge to a cell that does
// not belong to the caller
std::int32_t num_ghost_nodes = 0;
{
MPI_Wait(&request_offset_scan, MPI_STATUS_IGNORE);
std::array<std::int64_t, 2> range
= {offset_global, offset_global + num_owned};
std::vector<std::int64_t> ghost_edges;
std::copy_if(graph.array().begin(), graph.array().end(),
std::back_inserter(ghost_edges),
[range](auto e) { return e < range[0] or e >= range[1]; });
std::ranges::sort(ghost_edges);
auto it = std::ranges::unique(ghost_edges).begin();
num_ghost_nodes = std::distance(ghost_edges.begin(), it);
}
// Resize vector to hold node partition indices with enough extra
// space for ghost node partition information too. When there are no
// nodes, vertgstnbr may be zero, and at least one dummy location must
// be created.
const std::int32_t vertgstnbr = graph.num_nodes() + num_ghost_nodes;
std::vector<SCOTCH_Num> node_partition(std::max(1, vertgstnbr), 0);
// Partition the graph
common::Timer timer2("SCOTCH: call SCOTCH_dgraphPart");
err = SCOTCH_dgraphPart(&dgrafdat, nparts, &strat, node_partition.data());
if (err != 0)
throw std::runtime_error("Error during SCOTCH partitioning");
timer2.stop();
// Data arrays for adjacency list, where the edges are the destination
// ranks for each node
std::vector<std::int32_t> dests;
std::vector<std::int32_t> offsets(1, 0);
if (ghosting)
{
// Exchange halo with node_partition data for ghosts
common::Timer timer3("SCOTCH: call SCOTCH_dgraphHalo");
err = SCOTCH_dgraphHalo(&dgrafdat, node_partition.data(),
dolfinx::MPI::mpi_type<SCOTCH_Num>());
if (err != 0)
throw std::runtime_error("Error during SCOTCH halo exchange");
timer3.stop();
// Get SCOTCH's locally indexed graph
common::Timer timer4("Get SCOTCH graph data");
SCOTCH_Num* edge_ghost_tab;
SCOTCH_dgraphData(&dgrafdat, nullptr, nullptr, nullptr, nullptr, nullptr,
nullptr, nullptr, nullptr, nullptr, nullptr, nullptr,
nullptr, nullptr, &edge_ghost_tab, nullptr, &comm);
timer4.stop();
// Iterate through SCOTCH's local compact graph to find partition
// boundaries and save to map
common::Timer timer5("Extract partition boundaries from SCOTCH graph");
// Create a map of local nodes to their additional destination
// processes, due to ghosting
std::map<std::int32_t, std::set<std::int32_t>> local_node_to_dests;
for (std::int32_t node0 = 0; node0 < graph.num_nodes(); ++node0)
{
// Get all edges outward from node i
const std::int32_t node0_rank = node_partition[node0];
for (SCOTCH_Num j = vertloctab[node0]; j < vertloctab[node0 + 1]; ++j)
{
// Any edge which connects to a different partition will be a
// ghost
const std::int32_t node1_rank = node_partition[edge_ghost_tab[j]];
if (node0_rank != node1_rank)
local_node_to_dests[node0].insert(node1_rank);
}
}
timer5.stop();
offsets.reserve(graph.num_nodes() + 1);
for (std::int32_t i = 0; i < graph.num_nodes(); ++i)
{
dests.push_back(node_partition[i]);
if (auto it = local_node_to_dests.find(i);
it != local_node_to_dests.end())
{
dests.insert(dests.end(), it->second.begin(), it->second.end());
}
offsets.push_back(dests.size());
}
dests.shrink_to_fit();
}
else
{
offsets.resize(graph.num_nodes() + 1);
std::iota(offsets.begin(), offsets.end(), 0);
dests = std::vector<std::int32_t>(
node_partition.begin(),
std::next(node_partition.begin(), graph.num_nodes()));
}
// Clean up SCOTCH objects
SCOTCH_dgraphExit(&dgrafdat);
SCOTCH_stratExit(&strat);
return graph::AdjacencyList(std::move(dests), std::move(offsets));
};
}
#endif
//-----------------------------------------------------------------------------
#ifdef HAS_PARMETIS
graph::partition_fn graph::parmetis::partitioner(double imbalance,
std::array<int, 3> options)
{
return [imbalance, options](MPI_Comm comm, idx_t nparts,
const graph::AdjacencyList<std::int64_t>& graph,
bool ghosting)
{
spdlog::info("Compute graph partition using ParMETIS");
common::Timer timer("Compute graph partition (ParMETIS)");
if (nparts == 1 and dolfinx::MPI::size(comm) == 1)
{
// Nothing to be partitioned
return regular_adjacency_list(
std::vector<std::int32_t>(graph.num_nodes(), 0), 1);
}
// Note: ParMETIS fails (crashes) if a rank does not have any graph
// data. Therefore we split the communicator such that ParMETIS
// partitioning happens only on ranks that have data. Ideallt we
// wouldn't need to do this.
constexpr bool split_comm = true;
MPI_Comm pcomm = MPI_COMM_NULL;
if (split_comm)
{
int rank = dolfinx::MPI::rank(comm);
int color = graph.num_nodes() > 0 ? 1 : MPI_UNDEFINED;
int ierr = MPI_Comm_split(comm, color, rank, &pcomm);
dolfinx::MPI::check_error(comm, ierr);
}
else
pcomm = comm;
std::vector<idx_t> part(graph.num_nodes());
std::vector<idx_t> node_disp;
if (pcomm != MPI_COMM_NULL)
{
// Build adjacency list data
const int psize = dolfinx::MPI::size(pcomm);
const idx_t num_local_nodes = graph.num_nodes();
node_disp = std::vector<idx_t>(psize + 1, 0);
MPI_Allgather(&num_local_nodes, 1, dolfinx::MPI::mpi_type<idx_t>(),
node_disp.data() + 1, 1, dolfinx::MPI::mpi_type<idx_t>(),
pcomm);
std::partial_sum(node_disp.begin(), node_disp.end(), node_disp.begin());
std::vector<idx_t> array(graph.array().begin(), graph.array().end());
std::vector<idx_t> offsets(graph.offsets().begin(),
graph.offsets().end());
// Options and data for ParMETIS
std::array<idx_t, 3> opts = {options[0], options[1], options[2]};
idx_t ncon = 1;
idx_t* elmwgt = nullptr;
idx_t wgtflag(0), edgecut(0), numflag(0);
std::vector<real_t> tpwgts(ncon * nparts,
1.0 / static_cast<real_t>(nparts));
real_t ubvec = static_cast<real_t>(imbalance);
// Partition
common::Timer timer1("ParMETIS: call ParMETIS_V3_PartKway");
int err = ParMETIS_V3_PartKway(
node_disp.data(), offsets.data(), array.data(), elmwgt, nullptr,
&wgtflag, &numflag, &ncon, &nparts, tpwgts.data(), &ubvec,
opts.data(), &edgecut, part.data(), &pcomm);
if (err != METIS_OK)
{
throw std::runtime_error("ParMETIS_V3_PartKway failed. Error code: "
+ std::to_string(err));
}
}
if (ghosting and pcomm != MPI_COMM_NULL)
{
// FIXME: Is it implicit that the first entry is the owner?
graph::AdjacencyList<int> dest
= compute_destination_ranks(pcomm, graph, node_disp, part);
if (split_comm)
MPI_Comm_free(&pcomm);
return dest;
}
else
{
if (split_comm and pcomm != MPI_COMM_NULL)
MPI_Comm_free(&pcomm);
return regular_adjacency_list(std::vector<int>(part.begin(), part.end()),
1);
}
};
}
//-----------------------------------------------------------------------------
#endif
#ifdef HAS_KAHIP
//----------------------------------------------------------------------------
graph::partition_fn graph::kahip::partitioner(int mode, int seed,
double imbalance,
bool suppress_output)
{
return [mode, seed, imbalance, suppress_output](
MPI_Comm comm, int nparts,
const graph::AdjacencyList<std::int64_t>& graph, bool ghosting)
{
spdlog::info("Compute graph partition using (parallel) KaHIP");
// KaHIP integer type
using T = unsigned long long;
common::Timer timer("Compute graph partition (KaHIP)");
// Graph does not have vertex or adjacency weights, so we use null
// pointers as arguments
T *vwgt(nullptr), *adjcwgt(nullptr);
// Build adjacency list data
common::Timer timer1("KaHIP: build adjacency data");
std::vector<T> node_disp(dolfinx::MPI::size(comm) + 1, 0);
const T num_local_nodes = graph.num_nodes();
MPI_Allgather(&num_local_nodes, 1, dolfinx::MPI::mpi_type<T>(),
node_disp.data() + 1, 1, dolfinx::MPI::mpi_type<T>(), comm);
std::partial_sum(node_disp.begin(), node_disp.end(), node_disp.begin());
std::vector<T> array(graph.array().begin(), graph.array().end());
std::vector<T> offsets(graph.offsets().begin(), graph.offsets().end());
timer1.stop();
// Call KaHIP to partition graph
common::Timer timer2("KaHIP: call ParHIPPartitionKWay");
std::vector<T> part(graph.num_nodes());
int edgecut = 0;
double _imbalance = imbalance;
ParHIPPartitionKWay(node_disp.data(), offsets.data(), array.data(), vwgt,
adjcwgt, &nparts, &_imbalance, suppress_output, seed,
mode, &edgecut, part.data(), &comm);
timer2.stop();
if (ghosting)
return compute_destination_ranks(comm, graph, node_disp, part);
else
{
return regular_adjacency_list(std::vector<int>(part.begin(), part.end()),
1);
}
};
}
//----------------------------------------------------------------------------
#endif
|