DOLFINx 0.12.0.0
DOLFINx C++
Loading...
Searching...
No Matches
MatrixCSR.h
1// Copyright (C) 2021-2022 Garth N. Wells and Chris N. Richardson
2//
3// This file is part of DOLFINx (https://www.fenicsproject.org)
4//
5// SPDX-License-Identifier: LGPL-3.0-or-later
6
7#pragma once
8
9#include "SparsityPattern.h"
10#include "Vector.h"
11#include "matrix_csr_impl.h"
12#include <algorithm>
13#include <dolfinx/common/IndexMap.h>
14#include <dolfinx/common/MPI.h>
15#include <dolfinx/graph/AdjacencyList.h>
16#include <mpi.h>
17#include <numeric>
18#include <span>
19#include <utility>
20#include <vector>
21
22// Define requirements on sparsity pattern required for MatrixCSR constructor
23// allowing alternative implementations that can provide these essentials.
24template <typename T>
25concept SparsityImplementation = requires(T sp, int i) {
26 { sp.graph() };
27 requires std::forward_iterator<typename decltype(sp.graph().first)::iterator>;
28 requires std::convertible_to<std::int32_t,
29 typename decltype(sp.graph().first)::value_type>;
30 requires std::forward_iterator<
31 typename decltype(sp.graph().second)::iterator>;
32 requires std::convertible_to<
33 std::int64_t, typename decltype(sp.graph().second)::value_type>;
34
35 { sp.block_size(i) } -> std::same_as<int>;
36 {
37 sp.index_map(i)
38 } -> std::same_as<std::shared_ptr<const dolfinx::common::IndexMap>>;
39};
40
41namespace dolfinx::la
42{
44enum class BlockMode : int
45{
46 compact = 0,
51};
52
67template <typename Scalar, typename Container = std::vector<Scalar>,
68 typename ColContainer = std::vector<std::int32_t>,
69 typename RowPtrContainer = std::vector<std::int64_t>>
70class MatrixCSR
71{
72 static_assert(std::is_same_v<typename Container::value_type, Scalar>);
73 static_assert(std::is_integral_v<typename ColContainer::value_type>);
74 static_assert(std::is_integral_v<typename RowPtrContainer::value_type>);
75
76 template <typename, typename, typename, typename>
77 friend class MatrixCSR;
78
79public:
81 using value_type = Scalar;
82
84 using container_type = Container;
85
87 using column_container_type = ColContainer;
88
90 using rowptr_container_type = RowPtrContainer;
91
115 template <int BS0 = 1, int BS1 = 1>
117 {
118 if ((BS0 != _bs[0] and BS0 > 1 and _bs[0] > 1)
119 or (BS1 != _bs[1] and BS1 > 1 and _bs[1] > 1))
120 {
121 throw std::runtime_error(
122 "Cannot insert blocks of different size than matrix block size");
123 }
124
125 return [this](std::span<const std::int32_t> rows,
126 std::span<const std::int32_t> cols,
127 std::span<const value_type> data) -> int
128 {
129 this->set<BS0, BS1>(data, rows, cols);
130 return 0;
131 };
132 }
133
157 template <int BS0 = 1, int BS1 = 1>
159 {
160 if ((BS0 != _bs[0] and BS0 > 1 and _bs[0] > 1)
161 or (BS1 != _bs[1] and BS1 > 1 and _bs[1] > 1))
162 {
163 throw std::runtime_error(
164 "Cannot insert blocks of different size than matrix block size");
165 }
166
167 return [this](std::span<const std::int32_t> rows,
168 std::span<const std::int32_t> cols,
169 std::span<const value_type> data) -> int
170 {
171 this->add<BS0, BS1>(data, rows, cols);
172 return 0;
173 };
174 }
175
199 template <SparsityImplementation T>
200 MatrixCSR(const T& p, BlockMode mode = BlockMode::compact);
201
204 MatrixCSR(MatrixCSR&& A) = default;
205
208 MatrixCSR(const MatrixCSR& A) = default;
209
223 template <typename Scalar0, typename Container0, typename ColContainer0,
224 typename RowPtrContainer0>
225 explicit MatrixCSR(
226 const MatrixCSR<Scalar0, Container0, ColContainer0, RowPtrContainer0>& A)
227 : _index_maps(A._index_maps), _block_mode(A.block_mode()),
228 _bs(A.block_size()), _data(A._data.begin(), A._data.end()),
229 _cols(A.cols().begin(), A.cols().end()),
230 _row_ptr(A.row_ptr().begin(), A.row_ptr().end()),
231 _off_diagonal_offset(A.off_diag_offset().begin(),
232 A.off_diag_offset().end()),
233 _comm(A.comm()), _request(MPI_REQUEST_NULL), _unpack_pos(A._unpack_pos),
234 _val_send_disp(A._val_send_disp), _val_recv_disp(A._val_recv_disp),
235 _ghost_row_to_rank(A._ghost_row_to_rank), _finalized(A._finalized)
236 {
237 }
238
243 [[deprecated("Use std::ranges::fill(A.values(), v) instead.")]]
245 {
246 check_not_finalized();
247 std::ranges::fill(_data, x);
248 }
249
266 template <int BS0, int BS1>
267 void set(std::span<const value_type> x, std::span<const std::int32_t> rows,
268 std::span<const std::int32_t> cols)
269 {
270 check_not_finalized();
271 auto set_fn = [](value_type& y, const value_type& x) { y = x; };
272
273 std::int32_t num_rows
274 = _index_maps[0]->size_local() + _index_maps[0]->num_ghosts();
275 assert(x.size() == rows.size() * cols.size() * BS0 * BS1);
276 if (_bs[0] == BS0 and _bs[1] == BS1)
277 {
278 impl::insert_csr<BS0, BS1>(_data, _cols, _row_ptr, x, rows, cols, set_fn,
279 num_rows);
280 }
281 else if (_bs[0] == 1 and _bs[1] == 1)
282 {
283 // Set blocked data in a regular CSR matrix (_bs[0]=1, _bs[1]=1)
284 // with correct sparsity
285 impl::insert_blocked_csr<BS0, BS1>(_data, _cols, _row_ptr, x, rows, cols,
286 set_fn, num_rows);
287 }
288 else
289 {
290 assert(BS0 == 1 and BS1 == 1);
291 // Set non-blocked data in a blocked CSR matrix (BS0=1, BS1=1)
292 impl::insert_nonblocked_csr(_data, _cols, _row_ptr, x, rows, cols, set_fn,
293 num_rows, _bs[0], _bs[1]);
294 }
295 }
296
312 template <int BS0 = 1, int BS1 = 1>
313 void add(std::span<const value_type> x, std::span<const std::int32_t> rows,
314 std::span<const std::int32_t> cols)
315 {
316 check_not_finalized();
317 auto add_fn = [](value_type& y, const value_type& x) { y += x; };
318
319 assert(x.size() == rows.size() * cols.size() * BS0 * BS1);
320 if (_bs[0] == BS0 and _bs[1] == BS1)
321 {
322 impl::insert_csr<BS0, BS1>(_data, _cols, _row_ptr, x, rows, cols, add_fn,
323 _row_ptr.size());
324 }
325 else if (_bs[0] == 1 and _bs[1] == 1)
326 {
327 // Add blocked data to a regular CSR matrix (_bs[0]=1, _bs[1]=1)
328 impl::insert_blocked_csr<BS0, BS1>(_data, _cols, _row_ptr, x, rows, cols,
329 add_fn, _row_ptr.size());
330 }
331 else
332 {
333 assert(BS0 == 1 and BS1 == 1);
334 // Add non-blocked data to a blocked CSR matrix (BS0=1, BS1=1)
335 impl::insert_nonblocked_csr(_data, _cols, _row_ptr, x, rows, cols, add_fn,
336 _row_ptr.size(), _bs[0], _bs[1]);
337 }
338 }
339
341 std::int32_t num_owned_rows() const { return _index_maps[0]->size_local(); }
342
344 std::int32_t num_all_rows() const { return _row_ptr.size() - 1; }
345
355 std::vector<value_type> to_dense() const
356 {
357 const std::size_t nrows = num_all_rows();
358 const std::size_t ncols = _index_maps[1]->size_global();
359 std::vector<value_type> A(nrows * ncols * _bs[0] * _bs[1], value_type(0));
360 for (std::size_t r = 0; r < nrows; ++r)
361 {
362 for (std::int32_t j = _row_ptr[r]; j < _row_ptr[r + 1]; ++j)
363 {
364 for (int i0 = 0; i0 < _bs[0]; ++i0)
365 {
366 for (int i1 = 0; i1 < _bs[1]; ++i1)
367 {
368 std::array<std::int32_t, 1> local_col{_cols[j]};
369 std::array<std::int64_t, 1> global_col{0};
370 _index_maps[1]->local_to_global(local_col, global_col);
371 A[(r * _bs[0] + i0) * ncols * _bs[1] + global_col[0] * _bs[1] + i1]
372 = _data[j * _bs[0] * _bs[1] + i0 * _bs[1] + i1];
373 }
374 }
375 }
376 }
377
378 return A;
379 }
380
388 {
391 }
392
403 {
404 check_not_finalized();
405 const std::int32_t local_size0 = _index_maps[0]->size_local();
406 const std::int32_t num_ghosts0 = _index_maps[0]->num_ghosts();
407 const int bs2 = _bs[0] * _bs[1];
408
409 // For each ghost row, pack and send values to send to neighborhood
410 std::vector<int> insert_pos = _val_send_disp;
411 _ghost_value_data.resize(_val_send_disp.back());
412 for (int i = 0; i < num_ghosts0; ++i)
413 {
414 int rank = _ghost_row_to_rank[i];
415
416 // Get position in send buffer to place data to send to this
417 // neighbour
418 std::int32_t val_pos = insert_pos[rank];
419 std::copy(std::next(_data.data(), _row_ptr[local_size0 + i] * bs2),
420 std::next(_data.data(), _row_ptr[local_size0 + i + 1] * bs2),
421 std::next(_ghost_value_data.begin(), val_pos));
422 insert_pos[rank]
423 += bs2 * (_row_ptr[local_size0 + i + 1] - _row_ptr[local_size0 + i]);
424 }
425
426 _ghost_value_data_in.resize(_val_recv_disp.back());
427
428 // Compute data sizes for send and receive from displacements
429 std::vector<int> val_send_count(_val_send_disp.size() - 1);
430 std::adjacent_difference(std::next(_val_send_disp.begin()),
431 _val_send_disp.end(), val_send_count.begin());
432
433 std::vector<int> val_recv_count(_val_recv_disp.size() - 1);
434 std::adjacent_difference(std::next(_val_recv_disp.begin()),
435 _val_recv_disp.end(), val_recv_count.begin());
436
437 int status = MPI_Ineighbor_alltoallv(
438 _ghost_value_data.data(), val_send_count.data(), _val_send_disp.data(),
439 dolfinx::MPI::mpi_t<value_type>, _ghost_value_data_in.data(),
440 val_recv_count.data(), _val_recv_disp.data(),
441 dolfinx::MPI::mpi_t<value_type>, _comm.comm(), &_request);
442 dolfinx::MPI::check_error(_comm.comm(), status);
443 }
444
451 {
452 check_not_finalized();
453 int status = MPI_Wait(&_request, MPI_STATUS_IGNORE);
454 dolfinx::MPI::check_error(_comm.comm(), status);
455
456 _ghost_value_data.clear();
457 _ghost_value_data.shrink_to_fit();
458
459 // Add to local rows
460 int bs2 = _bs[0] * _bs[1];
461 assert(_ghost_value_data_in.size() == _unpack_pos.size() * bs2);
462 for (std::size_t i = 0; i < _unpack_pos.size(); ++i)
463 for (int j = 0; j < bs2; ++j)
464 _data[_unpack_pos[i] * bs2 + j] += _ghost_value_data_in[i * bs2 + j];
465
466 _ghost_value_data_in.clear();
467 _ghost_value_data_in.shrink_to_fit();
468
469 // Set ghost row data to zero
470 std::int32_t local_size0 = _index_maps[0]->size_local();
471 std::fill(std::next(_data.begin(), _row_ptr[local_size0] * bs2),
472 _data.end(), 0);
473 }
474
478 double squared_norm() const
479 {
480 const std::size_t num_owned_rows = _index_maps[0]->size_local();
481 const int bs2 = _bs[0] * _bs[1];
482 assert(num_owned_rows < _row_ptr.size());
483 double norm_sq_local = std::accumulate(
484 _data.cbegin(),
485 std::next(_data.cbegin(), _row_ptr[num_owned_rows] * bs2), double(0),
486 [](auto norm, value_type y) { return norm + std::norm(y); });
487 double norm_sq;
488 MPI_Allreduce(&norm_sq_local, &norm_sq, 1, MPI_DOUBLE, MPI_SUM,
489 _comm.comm());
490 return norm_sq;
491 }
492
503 void mult(Vector<value_type>& x, Vector<value_type>& y) const;
504
536
538 MPI_Comm comm() const { return _comm.comm(); }
539
547 std::shared_ptr<const common::IndexMap> index_map(int dim) const
548 {
549 return _index_maps.at(dim);
550 }
551
554 container_type& values() { return _data; }
555
558 const container_type& values() const { return _data; }
559
562 const rowptr_container_type& row_ptr() const { return _row_ptr; }
563
566 const column_container_type& cols() const { return _cols; }
567
578 {
579 return _off_diagonal_offset;
580 }
581
584 std::array<int, 2> block_size() const { return _bs; }
585
587 BlockMode block_mode() const { return _block_mode; }
588
608 {
609 // Remove any zero entries (blocks, where all entries in the block
610 // are within tolerance of zero) in data, and update the column
611 // indices and row pointers accordingly.
612 const std::size_t bs2 = _bs[0] * _bs[1];
613
614 // True if every entry of the block starting at block index j is
615 // within tolerance of zero, i.e. the whole block can be dropped.
616 auto is_zero_block = [this, bs2, tol](std::int64_t j)
617 {
618 return std::all_of(std::next(_data.begin(), j * bs2),
619 std::next(_data.begin(), (j + 1) * bs2),
620 [tol](value_type x)
621 { return std::abs(x) <= std::abs(tol); });
622 };
623
624 std::int64_t ptr_out = 0;
625 std::vector<std::int64_t> new_row_ptr = {0};
626 std::vector<std::int64_t> new_off_diagonal_offset;
627 new_row_ptr.reserve(_row_ptr.size());
628 new_off_diagonal_offset.reserve(_off_diagonal_offset.size());
629 for (std::size_t i = 0; i < _row_ptr.size() - 1; ++i)
630 {
631 for (std::int64_t j = _row_ptr[i]; j < _off_diagonal_offset[i]; ++j)
632 {
633 if (!is_zero_block(j))
634 {
635 _cols[ptr_out] = _cols[j];
636 std::copy_n(std::next(_data.begin(), j * bs2), bs2,
637 std::next(_data.begin(), ptr_out * bs2));
638 ++ptr_out;
639 }
640 }
641 new_off_diagonal_offset.push_back(ptr_out);
642 for (std::int64_t j = _off_diagonal_offset[i]; j < _row_ptr[i + 1]; ++j)
643 {
644 if (!is_zero_block(j))
645 {
646 _cols[ptr_out] = _cols[j];
647 std::copy_n(std::next(_data.begin(), j * bs2), bs2,
648 std::next(_data.begin(), ptr_out * bs2));
649 ++ptr_out;
650 }
651 }
652 new_row_ptr.push_back(ptr_out);
653 }
654 _data.resize(ptr_out * bs2);
655 _cols.resize(ptr_out);
656 _row_ptr = new_row_ptr;
657 _off_diagonal_offset = new_off_diagonal_offset;
658 _finalized = true;
659 }
660
661private:
662 // Parallel distribution of the rows and columns
663 std::array<std::shared_ptr<const common::IndexMap>, 2> _index_maps;
664
665 // Block mode (compact or expanded)
666 BlockMode _block_mode;
667
668 // Block sizes
669 std::array<int, 2> _bs;
670
671 // Matrix data
672 container_type _data;
674 rowptr_container_type _row_ptr;
675
676 // Start of off-diagonal (unowned columns) on each row
677 rowptr_container_type _off_diagonal_offset;
678
679 // Communicator with neighborhood (ghost->owner communicator for rows)
680 dolfinx::MPI::Comm _comm;
681
682 // -- Precomputed data for scatter_rev/update
683
684 // Request in non-blocking communication
685 MPI_Request _request;
686
687 // Position in _data to add received data
688 std::vector<std::size_t> _unpack_pos;
689
690 // Displacements for alltoall for each neighbor when sending and
691 // receiving
692 std::vector<int> _val_send_disp, _val_recv_disp;
693
694 // Ownership of each row, by neighbor (for the neighbourhood defined
695 // on _comm)
696 std::vector<int> _ghost_row_to_rank;
697
698 // Temporary stores for data during non-blocking communication
699 container_type _ghost_value_data;
700 container_type _ghost_value_data_in;
701
702 // Set by eliminate_zeros(). Once true, the sparsity may have been
703 // reduced and the precomputed scatter_rev communication pattern
704 // (_unpack_pos, _val_send_disp, _val_recv_disp) is no longer valid,
705 // so further modification of the matrix is disallowed.
706 bool _finalized = false;
707
708 // Throw if the matrix has been finalized by eliminate_zeros().
709 void check_not_finalized() const
710 {
711 if (_finalized)
712 {
713 throw std::runtime_error(
714 "MatrixCSR has been finalized by eliminate_zeros() and can no "
715 "longer be modified or scattered.");
716 }
717 }
718};
719//-----------------------------------------------------------------------------
720
722template <typename U, typename V, typename W, typename X>
723template <SparsityImplementation SparsityType>
724MatrixCSR<U, V, W, X>::MatrixCSR(const SparsityType& p, BlockMode mode)
725 : _index_maps({p.index_map(0), p.index_map(1)}), _block_mode(mode),
726 _bs({p.block_size(0), p.block_size(1)}),
727 _data(p.graph().first.size() * _bs[0] * _bs[1], 0),
728 _cols(p.graph().first.begin(), p.graph().first.end()),
729 _row_ptr(p.graph().second.begin(), p.graph().second.end()),
730 _comm(MPI_COMM_NULL)
731{
732 if (_block_mode == BlockMode::expanded)
733 {
734 // Rebuild IndexMaps
735 for (int i = 0; i < 2; ++i)
736 {
737 auto im = _index_maps[i];
738 std::int32_t size_local = im->size_local() * _bs[i];
739 std::span ghost_i = im->ghosts();
740 std::vector<std::int64_t> ghosts;
741 const std::vector<int> ghost_owner_i(im->owners().begin(),
742 im->owners().end());
743 std::vector<int> src_rank;
744 for (std::size_t j = 0; j < ghost_i.size(); ++j)
745 {
746 for (int k = 0; k < _bs[i]; ++k)
747 {
748 ghosts.push_back(ghost_i[j] * _bs[i] + k);
749 src_rank.push_back(ghost_owner_i[j]);
750 }
751 }
752
753 std::array<std::vector<int>, 2> src_dest0
754 = {std::vector(_index_maps[i]->src().begin(),
755 _index_maps[i]->src().end()),
756 std::vector(_index_maps[i]->dest().begin(),
757 _index_maps[i]->dest().end())};
758 _index_maps[i] = std::make_shared<common::IndexMap>(
759 _index_maps[i]->comm(), size_local, src_dest0, ghosts, src_rank);
760 }
761
762 // Convert sparsity pattern and set _bs to 1
763
764 column_container_type new_cols;
765 new_cols.reserve(_data.size());
766 rowptr_container_type new_row_ptr{0};
767 new_row_ptr.reserve(_row_ptr.size() * _bs[0]);
768 std::span<const std::int32_t> num_diag_nnz = p.off_diagonal_offsets();
769 for (std::size_t i = 0; i < _row_ptr.size() - 1; ++i)
770 {
771 // Repeat row _bs[0] times
772 for (int q0 = 0; q0 < _bs[0]; ++q0)
773 {
774 _off_diagonal_offset.push_back(new_row_ptr.back()
775 + num_diag_nnz[i] * _bs[1]);
776 for (auto j = _row_ptr[i]; j < _row_ptr[i + 1]; ++j)
777 {
778 for (int q1 = 0; q1 < _bs[1]; ++q1)
779 new_cols.push_back(_cols[j] * _bs[1] + q1);
780 }
781 new_row_ptr.push_back(new_cols.size());
782 }
783 }
784 _cols = new_cols;
785 _row_ptr = new_row_ptr;
786 _bs[0] = 1;
787 _bs[1] = 1;
788 }
789 else
790 {
791 // Compute off-diagonal offset for each row (compact)
792 std::span<const std::int32_t> num_diag_nnz = p.off_diagonal_offsets();
793 _off_diagonal_offset.reserve(num_diag_nnz.size());
794 std::ranges::transform(num_diag_nnz, _row_ptr,
795 std::back_inserter(_off_diagonal_offset),
796 std::plus{});
797 }
798
799 // Some short-hand
800 std::array local_size
801 = {_index_maps[0]->size_local(), _index_maps[1]->size_local()};
802 std::array local_range
803 = {_index_maps[0]->local_range(), _index_maps[1]->local_range()};
804 std::span ghosts1 = _index_maps[1]->ghosts();
805
806 std::span ghosts0 = _index_maps[0]->ghosts();
807 std::span src_ranks = _index_maps[0]->src();
808 std::span dest_ranks = _index_maps[0]->dest();
809
810 // Create neighbourhood communicator (owner <- ghost)
811 MPI_Comm comm;
812 MPI_Dist_graph_create_adjacent(_index_maps[0]->comm(), dest_ranks.size(),
813 dest_ranks.data(), MPI_UNWEIGHTED,
814 src_ranks.size(), src_ranks.data(),
815 MPI_UNWEIGHTED, MPI_INFO_NULL, false, &comm);
816 _comm = dolfinx::MPI::Comm(comm, false);
817
818 // Build map from ghost row index position to owning (neighborhood)
819 // rank
820 _ghost_row_to_rank.reserve(_index_maps[0]->owners().size());
821 for (int r : _index_maps[0]->owners())
822 {
823 auto it = std::ranges::lower_bound(src_ranks, r);
824 assert(it != src_ranks.end() and *it == r);
825 std::size_t pos = std::ranges::distance(src_ranks.begin(), it);
826 _ghost_row_to_rank.push_back(pos);
827 }
828
829 // Compute size of data to send to each neighbor
830 std::vector<std::int32_t> data_per_proc(src_ranks.size(), 0);
831 for (std::size_t i = 0; i < _ghost_row_to_rank.size(); ++i)
832 {
833 assert(_ghost_row_to_rank[i] < (int)data_per_proc.size());
834 std::size_t pos = local_size[0] + i;
835 data_per_proc[_ghost_row_to_rank[i]] += _row_ptr[pos + 1] - _row_ptr[pos];
836 }
837
838 // Compute send displacements
839 _val_send_disp.resize(src_ranks.size() + 1, 0);
840 std::partial_sum(data_per_proc.begin(), data_per_proc.end(),
841 std::next(_val_send_disp.begin()));
842
843 // For each ghost row, pack and send indices to neighborhood
844 std::vector<std::int64_t> ghost_index_data(2 * _val_send_disp.back());
845 {
846 std::vector<int> insert_pos = _val_send_disp;
847 for (std::size_t i = 0; i < _ghost_row_to_rank.size(); ++i)
848 {
849 int rank = _ghost_row_to_rank[i];
850 std::int32_t row_id = local_size[0] + i;
851 for (int j = _row_ptr[row_id]; j < _row_ptr[row_id + 1]; ++j)
852 {
853 // Get position in send buffer
854 std::int32_t idx_pos = 2 * insert_pos[rank];
855
856 // Pack send data (row, col) as global indices
857 ghost_index_data[idx_pos] = ghosts0[i];
858 if (std::int32_t col_local = _cols[j]; col_local < local_size[1])
859 ghost_index_data[idx_pos + 1] = col_local + local_range[1][0];
860 else
861 ghost_index_data[idx_pos + 1] = ghosts1[col_local - local_size[1]];
862
863 insert_pos[rank] += 1;
864 }
865 }
866 }
867
868 // Communicate data with neighborhood
869 std::vector<std::int64_t> ghost_index_array;
870 std::vector<int> recv_disp;
871 {
872 std::vector<int> send_sizes;
873 std::ranges::transform(data_per_proc, std::back_inserter(send_sizes),
874 [](auto x) { return 2 * x; });
875
876 std::vector<int> recv_sizes(dest_ranks.size());
877 send_sizes.reserve(1);
878 recv_sizes.reserve(1);
879 MPI_Neighbor_alltoall(send_sizes.data(), 1, MPI_INT, recv_sizes.data(), 1,
880 MPI_INT, _comm.comm());
881
882 // Build send/recv displacement
883 std::vector<int> send_disp{0};
884 std::partial_sum(send_sizes.begin(), send_sizes.end(),
885 std::back_inserter(send_disp));
886 recv_disp = {0};
887 std::partial_sum(recv_sizes.begin(), recv_sizes.end(),
888 std::back_inserter(recv_disp));
889
890 ghost_index_array.resize(recv_disp.back());
891 MPI_Neighbor_alltoallv(ghost_index_data.data(), send_sizes.data(),
892 send_disp.data(), MPI_INT64_T,
893 ghost_index_array.data(), recv_sizes.data(),
894 recv_disp.data(), MPI_INT64_T, _comm.comm());
895 }
896
897 // Store receive displacements for future use, when transferring
898 // data values
899 _val_recv_disp.resize(recv_disp.size());
900 int bs2 = _bs[0] * _bs[1];
901 std::ranges::transform(recv_disp, _val_recv_disp.begin(),
902 [&bs2](auto d) { return bs2 * d / 2; });
903 std::ranges::transform(_val_send_disp, _val_send_disp.begin(),
904 [&bs2](auto d) { return d * bs2; });
905
906 // Global-to-local map for ghost columns
907 std::vector<std::pair<std::int64_t, std::int32_t>> global_to_local;
908 global_to_local.reserve(ghosts1.size());
909 for (std::int64_t idx : ghosts1)
910 global_to_local.push_back({idx, global_to_local.size() + local_size[1]});
911 std::ranges::sort(global_to_local);
912
913 // Compute location in which data for each index should be stored
914 // when received
915 for (std::size_t i = 0; i < ghost_index_array.size(); i += 2)
916 {
917 // Row must be on this process
918 std::int32_t local_row = ghost_index_array[i] - local_range[0][0];
919 assert(local_row >= 0 and local_row < local_size[0]);
920
921 // Column may be owned or unowned
922 std::int32_t local_col = ghost_index_array[i + 1] - local_range[1][0];
923 if (local_col < 0 or local_col >= local_size[1])
924 {
925 auto it = std::ranges::lower_bound(
926 global_to_local, std::pair(ghost_index_array[i + 1], -1),
927 [](auto a, auto b) { return a.first < b.first; });
928 assert(it != global_to_local.end()
929 and it->first == ghost_index_array[i + 1]);
930 local_col = it->second;
931 }
932 auto cit0 = std::next(_cols.begin(), _row_ptr[local_row]);
933 auto cit1 = std::next(_cols.begin(), _row_ptr[local_row + 1]);
934
935 // Find position of column index and insert data
936 auto cit = std::lower_bound(cit0, cit1, local_col);
937 assert(cit != cit1);
938 assert(*cit == local_col);
939 std::size_t d = std::ranges::distance(_cols.begin(), cit);
940 _unpack_pos.push_back(d);
941 }
942
943 _unpack_pos.shrink_to_fit();
944}
945//-----------------------------------------------------------------------------
946
947// The matrix A is distributed across P processes by blocks of rows:
948// A = | A_0 |
949// | A_1 |
950// | ... |
951// | A_P-1 |
952//
953// Each submatrix A_i is owned by a single process "i" and can be further
954// decomposed into diagonal (Ai[0]) and off diagonal (Ai[1]) blocks:
955// Ai = |Ai[0] Ai[1]|
956//
957// If A is square, the diagonal block Ai[0] is also square and contains
958// only owned columns and rows. The block Ai[1] contains ghost columns
959// (unowned dofs).
960
961// Likewise, a local vector x can be decomposed into owned and ghost blocks:
962// xi = | x[0] |
963// | x[1] |
964//
965// So the product y = Ax can be computed into two separate steps:
966// y[0] = |Ai[0] Ai[1]| | x[0] | = Ai[0] x[0] + Ai[1] x[1]
967// | x[1] |
968//
971template <typename Scalar, typename V, typename W, typename X>
973 la::Vector<Scalar>& y) const
974{
975 // start communication (update ghosts)
977
978 std::int32_t nrowslocal = num_owned_rows();
979 std::span<const std::int64_t> Arow_ptr(row_ptr().data(), nrowslocal + 1);
980 std::span<const std::int32_t> Acols(cols().data(), Arow_ptr[nrowslocal]);
981 std::span<const std::int64_t> Aoff_diag_offset(off_diag_offset().data(),
982 nrowslocal);
983 std::span<const Scalar> Avalues(values().data(),
984 Arow_ptr[nrowslocal] * _bs[0] * _bs[1]);
985
986 std::span<const Scalar> _x = x.array();
987 std::span<Scalar> _y = y.array();
988
989 std::span<const std::int64_t> Arow_begin(Arow_ptr.data(), nrowslocal);
990 std::span<const std::int64_t> Arow_end(Arow_ptr.data() + 1, nrowslocal);
991
992 // First stage: spmv - diagonal
993 // yi[0] += Ai[0] * xi[0]
994 if (_bs[1] == 1)
995 {
996 impl::spmv<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
997 _bs[0], std::integral_constant<int, 1>{});
998 }
999 else if (_bs[1] == 2)
1000 {
1001 impl::spmv<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1002 _bs[0], std::integral_constant<int, 2>{});
1003 }
1004 else if (_bs[1] == 3)
1005 {
1006 impl::spmv<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1007 _bs[0], std::integral_constant<int, 3>{});
1008 }
1009 else
1010 {
1011 impl::spmv<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1012 _bs[0], _bs[1]);
1013 }
1014
1015 // finalize ghost update
1016 x.scatter_fwd_end();
1017
1018 // Second stage: spmv - off-diagonal
1019 // yi[0] += Ai[1] * xi[1]
1020 if (_bs[1] == 1)
1021 {
1022 impl::spmv<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1023 _bs[0], std::integral_constant<int, 1>{});
1024 }
1025 else if (_bs[1] == 2)
1026 {
1027 impl::spmv<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1028 _bs[0], std::integral_constant<int, 2>{});
1029 }
1030 else if (_bs[1] == 3)
1031 {
1032 impl::spmv<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1033 _bs[0], std::integral_constant<int, 3>{});
1034 }
1035 else
1036 {
1037 impl::spmv<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1038 _bs[0], _bs[1]);
1039 }
1040}
1041
1044template <typename Scalar, typename V, typename W, typename X>
1046 la::Vector<Scalar>& y) const
1047{
1048 std::int32_t nrowslocal = num_owned_rows();
1049 std::span<const std::int64_t> Arow_ptr(row_ptr().data(), nrowslocal + 1);
1050 std::span<const std::int32_t> Acols(cols().data(), Arow_ptr[nrowslocal]);
1051 std::span<const std::int64_t> Aoff_diag_offset(off_diag_offset().data(),
1052 nrowslocal);
1053 std::span<const Scalar> Avalues(values().data(),
1054 Arow_ptr[nrowslocal] * _bs[0] * _bs[1]);
1055
1056 std::span<const Scalar> _x = x.array();
1057 std::span<Scalar> _y = y.array();
1058
1059 std::span<const std::int64_t> Arow_begin(Arow_ptr.data(), nrowslocal);
1060 std::span<const std::int64_t> Arow_end(Arow_ptr.data() + 1, nrowslocal);
1061
1062 // Compute ghost region contribution and scatter back. Zero only the
1063 // ghost portion of y so the caller's owned values are preserved (multT
1064 // accumulates).
1065 std::int32_t ncolslocal = index_map(1)->size_local();
1066 std::fill(std::next(_y.begin(), ncolslocal * _bs[1]), _y.end(), Scalar(0));
1067 if (_bs[1] == 1)
1068 {
1069 impl::spmvT<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1070 _bs[0], std::integral_constant<int, 1>{});
1071 }
1072 else if (_bs[1] == 2)
1073 {
1074 impl::spmvT<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1075 _bs[0], std::integral_constant<int, 2>{});
1076 }
1077 else if (_bs[1] == 3)
1078 {
1079 impl::spmvT<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1080 _bs[0], std::integral_constant<int, 3>{});
1081 }
1082 else
1083 {
1084 impl::spmvT<Scalar>(Avalues, Aoff_diag_offset, Arow_end, Acols, _x, _y,
1085 _bs[0], _bs[1]);
1086 }
1087
1088 y.scatter_rev(std::plus<Scalar>{});
1089
1090 if (_bs[1] == 1)
1091 {
1092 impl::spmvT<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1093 _bs[0], std::integral_constant<int, 1>{});
1094 }
1095 else if (_bs[1] == 2)
1096 {
1097 impl::spmvT<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1098 _bs[0], std::integral_constant<int, 2>{});
1099 }
1100 else if (_bs[1] == 3)
1101 {
1102 impl::spmvT<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1103 _bs[0], std::integral_constant<int, 3>{});
1104 }
1105 else
1106 {
1107 impl::spmvT<Scalar>(Avalues, Arow_begin, Aoff_diag_offset, Acols, _x, _y,
1108 _bs[0], _bs[1]);
1109 }
1110}
1111} // namespace dolfinx::la
A duplicate MPI communicator and manage lifetime of the communicator.
Definition MPI.h:45
MPI_Comm comm() const noexcept
Return the underlying MPI_Comm object.
Definition MPI.cpp:71
const container_type & values() const
Get local values (const version).
Definition MatrixCSR.h:558
std::shared_ptr< const common::IndexMap > index_map(int dim) const
Index map for the row or column space.
Definition MatrixCSR.h:547
const rowptr_container_type & off_diag_offset() const
Get the start of off-diagonal (unowned columns) on each row, allowing the matrix to be split (virtual...
Definition MatrixCSR.h:577
void set(std::span< const value_type > x, std::span< const std::int32_t > rows, std::span< const std::int32_t > cols)
Set values in the matrix.
Definition MatrixCSR.h:267
MatrixCSR(const MatrixCSR< Scalar0, Container0, ColContainer0, RowPtrContainer0 > &A)
Copy-convert matrix, possibly using to different container types.
Definition MatrixCSR.h:225
RowPtrContainer rowptr_container_type
Row pointer container type.
Definition MatrixCSR.h:90
void scatter_rev_end()
End transfer of ghost row data to owning ranks.
Definition MatrixCSR.h:450
container_type & values()
Get local data values.
Definition MatrixCSR.h:554
auto mat_add_values()
Insertion functor for adding values to a matrix. It is typically used in finite element assembly func...
Definition MatrixCSR.h:158
BlockMode block_mode() const
Get 'block mode'.
Definition MatrixCSR.h:587
void add(std::span< const value_type > x, std::span< const std::int32_t > rows, std::span< const std::int32_t > cols)
Accumulate values in the matrix.
Definition MatrixCSR.h:313
std::int32_t num_owned_rows() const
Number of local rows excluding ghost rows.
Definition MatrixCSR.h:341
ColContainer column_container_type
Column index container type.
Definition MatrixCSR.h:87
void mult(Vector< value_type > &x, Vector< value_type > &y) const
Compute the product y += Ax.
Definition MatrixCSR.h:972
MatrixCSR(MatrixCSR &&A)=default
MatrixCSR(const T &p, BlockMode mode=BlockMode::compact)
Create a distributed matrix.
double squared_norm() const
Compute the Frobenius norm squared across all processes.
Definition MatrixCSR.h:478
void scatter_rev()
Transfer ghost row data to the owning ranks accumulating received values on the owned rows,...
Definition MatrixCSR.h:387
void multT(Vector< value_type > &x, Vector< value_type > &y) const
Compute the product y += A^T x.
Definition MatrixCSR.h:1045
void eliminate_zeros(value_type tol=0)
Remove any zero entries in the matrix data.
Definition MatrixCSR.h:607
Container container_type
Matrix entries container type.
Definition MatrixCSR.h:84
Scalar value_type
Scalar type.
Definition MatrixCSR.h:81
void scatter_rev_begin()
Begin transfer of ghost row data to owning ranks, where it will be accumulated into existing owned ro...
Definition MatrixCSR.h:402
const column_container_type & cols() const
Definition MatrixCSR.h:566
void set(value_type x)
Set all non-zero local entries to a value, including entries in ghost rows.
Definition MatrixCSR.h:244
std::array< int, 2 > block_size() const
Get block sizes.
Definition MatrixCSR.h:584
std::int32_t num_all_rows() const
Number of local rows including ghost rows.
Definition MatrixCSR.h:344
const rowptr_container_type & row_ptr() const
Get local row pointers.
Definition MatrixCSR.h:562
std::vector< value_type > to_dense() const
Copy to a dense matrix.
Definition MatrixCSR.h:355
MPI_Comm comm() const
Get MPI communicator that matrix is defined on.
Definition MatrixCSR.h:538
MatrixCSR(const MatrixCSR &A)=default
auto mat_set_values()
Insertion functor for setting values in a matrix. It is typically used in finite element assembly fun...
Definition MatrixCSR.h:116
A vector that can be distributed across processes.
Definition Vector.h:50
container_type & array()
Get the process-local part of the vector.
Definition Vector.h:390
void scatter_rev(BinaryOperation op)
Scatter (send) of ghost data values to the owning process and assign/accumulate into the owned data e...
Definition Vector.h:375
void scatter_fwd_end(U unpack)
End scatter (send) of local data values that are ghosted on other processes.
Definition Vector.h:259
void scatter_fwd_begin(U pack, GetPtr get_ptr)
Begin scatter (send) of local data that is ghosted on other processes.
Definition Vector.h:222
Definition MatrixCSR.h:25
MPI_Datatype mpi_t
Retrieves the MPI data type associated to the provided type.
Definition MPI.h:320
void check_error(MPI_Comm comm, int code)
Check MPI error code. If the error code is not equal to MPI_SUCCESS, then std::abort is called.
Definition MPI.cpp:89
int size(MPI_Comm comm)
Definition MPI.cpp:81
int rank(MPI_Comm comm)
Return process rank for the communicator.
Definition MPI.cpp:73
constexpr std::array< std::int64_t, 2 > local_range(int index, std::int64_t N, int size)
Partition a global range [0, N - 1] across callers into non-overlapping sub-partitions of almost equa...
Definition local_range.h:26
Linear algebra interface.
Definition dolfinx_la.h:7
BlockMode
Modes for representing block structured matrices.
Definition MatrixCSR.h:45
@ expanded
Definition MatrixCSR.h:48
auto norm(const V &x, Norm type=Norm::l2)
Compute the norm of the vector.
Definition Vector.h:480