Create submatrix from Index sets #964

pratikvn · 2022-02-04T14:16:09Z

This PR adds functionality to create submatrices from IndexSet objects, allowing one to create submatrices not only from contiguous spans, but also with dis-contiguous sets of indices.

Currently, only CSR is supported

Some index set related changes were also made:

Make index set a non-polymorphic class.
Rename IndexSet to index_set

TODO

Remove the workaround and pre-compute the local index array to use it in the computations

pratikvn · 2022-02-15T20:03:59Z

format!

codecov · 2022-02-16T04:56:09Z

Codecov Report

Merging #964 (43545a0) into develop (4430fb8) will decrease coverage by 1.13%.
The diff coverage is 96.09%.

@@             Coverage Diff             @@
##           develop     #964      +/-   ##
===========================================
- Coverage    93.41%   92.28%   -1.14%     
===========================================
  Files          479      479              
  Lines        39929    40352     +423     
===========================================
- Hits         37299    37238      -61     
- Misses        2630     3114     +484

Impacted Files	Coverage Δ
common/unified/base/index_set_kernels.cpp	`100.00% <ø> (ø)`
core/device_hooks/common_kernels.inc.cpp	`0.00% <0.00%> (ø)`
include/ginkgo/core/matrix/csr.hpp	`45.53% <ø> (ø)`
omp/base/index_set_kernels.cpp	`94.11% <ø> (+7.63%)`	⬆️
include/ginkgo/core/base/index_set.hpp	`82.81% <80.39%> (+14.63%)`	⬆️
reference/base/index_set_kernels.cpp	`94.20% <83.33%> (-5.80%)`	⬇️
core/base/index_set.cpp	`97.72% <100.00%> (+6.23%)`	⬆️
core/matrix/csr.cpp	`94.89% <100.00%> (-0.52%)`	⬇️
omp/matrix/csr_kernels.cpp	`84.43% <100.00%> (+2.48%)`	⬆️
omp/test/base/index_set.cpp	`100.00% <100.00%> (ø)`
... and 27 more

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yhmtsai

some nit and unused parameter needs to be deleted

reference/base/index_set_kernels.cpp

reference/matrix/csr_kernels.cpp

reference/test/matrix/csr_kernels.cpp

.github/abidiff.sh

upsj

There are some subtle issues with the algorithms that should be addressed.

core/base/index_set.cpp

include/ginkgo/core/base/index_set.hpp

core/base/index_set.cpp

include/ginkgo/core/base/index_set.hpp

omp/base/index_set_kernels.cpp

upsj · 2022-02-16T10:37:32Z

omp/base/index_set_kernels.cpp

+        const auto bucket = std::distance(
+            subset_begin,
+            std::upper_bound(subset_begin, subset_begin + num_subsets, index));


shouldn't this be using subset_end? Then you also won't need the following line

I think that is more or less equivalent ? I think you need to have a shifted index anyway to access the superset_indices later.

yes, I guess so. If I read upper_bound, I am thinking: you are looking for something that is larger than the entry, and subset_end would be less surprising

omp/base/index_set_kernels.cpp

omp/matrix/csr_kernels.cpp

stale

yhmtsai

there are some unused parameters. compute_submatrix_from_index_set is directly tested in omp but not reference. also some performance comments

core/matrix/csr.cpp

include/ginkgo/core/base/index_set.hpp

omp/base/index_set_kernels.cpp

omp/test/matrix/csr_kernels.cpp

reference/base/index_set_kernels.cpp

reference/matrix/csr_kernels.cpp

reference/test/matrix/csr_kernels.cpp

omp/matrix/csr_kernels.cpp

omp/test/matrix/csr_kernels.cpp

stale

Co-authored-by: Pratik Nayak <[email protected]>

Co-authored-by: Yu-Hsiang Tsai <[email protected]> Co-authored-by: Tobias Ribizel <[email protected]>

Co-authored-by: Yuhsiang Tsai <[email protected]>

Co-authored-by: Yu-Hsiang Tsai <[email protected]>

Co-authored-by: Tobias Ribizel <[email protected]> Co-authored-by: Marcel Koch <[email protected]>

include/ginkgo/core/base/index_set.hpp

upsj

LGTM! Only I don't think we need an executor-less index_set

include/ginkgo/core/base/index_set.hpp

Co-authored-by: Tobias Ribizel<[email protected]>

ginkgo-bot · 2022-03-29T06:59:40Z

Note: This PR changes the Ginkgo ABI:

Functions changes summary: 200 Removed, 0 Changed (32 filtered out), 154 Added functions
Variables changes summary: 0 Removed, 0 Changed, 0 Added variable

For details check the full ABI diff under Artifacts here

sonarcloud · 2022-03-30T08:41:54Z

SonarCloud Quality Gate failed.

0 Bugs
0 Vulnerabilities
0 Security Hotspots
28 Code Smells

71.4% Coverage
15.9% Duplication

Advertise release 1.5.0 and last changes + Add changelog, + Update third party libraries + A small fix to a CMake file See PR: #1195 The Ginkgo team is proud to announce the new Ginkgo minor release 1.5.0. This release brings many important new features such as: - MPI-based multi-node support for all matrix formats and most solvers; - full DPC++/SYCL support, - functionality and interface for GPU-resident sparse direct solvers, - an interface for wrapping solvers with scaling and reordering applied, - a new algebraic Multigrid solver/preconditioner, - improved mixed-precision support, - support for device matrix assembly, and much more. If you face an issue, please first check our [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues) and the [open issues list](https://github.com/ginkgo-project/ginkgo/issues) and if you do not find a solution, feel free to [open a new issue](https://github.com/ginkgo-project/ginkgo/issues/new/choose) or ask a question using the [github discussions](https://github.com/ginkgo-project/ginkgo/discussions). Supported systems and requirements: + For all platforms, CMake 3.13+ + C++14 compliant compiler + Linux and macOS + GCC: 5.5+ + clang: 3.9+ + Intel compiler: 2018+ + Apple LLVM: 8.0+ + NVHPC: 22.7+ + Cray Compiler: 14.0.1+ + CUDA module: CUDA 9.2+ or NVHPC 22.7+ + HIP module: ROCm 4.0+ + DPC++ module: Intel OneAPI 2021.3 with oneMKL and oneDPL. Set the CXX compiler to `dpcpp`. + Windows + MinGW and Cygwin: GCC 5.5+ + Microsoft Visual Studio: VS 2019 + CUDA module: CUDA 9.2+, Microsoft Visual Studio + OpenMP module: MinGW or Cygwin. Algorithm and important feature additions: + Add MPI-based multi-node for all matrix formats and solvers (except GMRES and IDR). ([#676](#676), [#908](#908), [#909](#909), [#932](#932), [#951](#951), [#961](#961), [#971](#971), [#976](#976), [#985](#985), [#1007](#1007), [#1030](#1030), [#1054](#1054), [#1100](#1100), [#1148](#1148)) + Porting the remaining algorithms (preconditioners like ISAI, Jacobi, Multigrid, ParILU(T) and ParIC(T)) to DPC++/SYCL, update to SYCL 2020, and improve support and performance ([#896](#896), [#924](#924), [#928](#928), [#929](#929), [#933](#933), [#943](#943), [#960](#960), [#1057](#1057), [#1110](#1110), [#1142](#1142)) + Add a Sparse Direct interface supporting GPU-resident numerical LU factorization, symbolic Cholesky factorization, improved triangular solvers, and more ([#957](#957), [#1058](#1058), [#1072](#1072), [#1082](#1082)) + Add a ScaleReordered interface that can wrap solvers and automatically apply reorderings and scalings ([#1059](#1059)) + Add a Multigrid solver and improve the aggregation based PGM coarsening scheme ([#542](#542), [#913](#913), [#980](#980), [#982](#982), [#986](#986)) + Add infrastructure for unified, lambda-based, backend agnostic, kernels and utilize it for some simple kernels ([#833](#833), [#910](#910), [#926](#926)) + Merge different CUDA, HIP, DPC++ and OpenMP tests under a common interface ([#904](#904), [#973](#973), [#1044](#1044), [#1117](#1117)) + Add a device_matrix_data type for device-side matrix assembly ([#886](#886), [#963](#963), [#965](#965)) + Add support for mixed real/complex BLAS operations ([#864](#864)) + Add a FFT LinOp for all but DPC++/SYCL ([#701](#701)) + Add FBCSR support for NVIDIA and AMD GPUs and CPUs with OpenMP ([#775](#775)) + Add CSR scaling ([#848](#848)) + Add array::const_view and equivalent to create constant matrices from non-const data ([#890](#890)) + Add a RowGatherer LinOp supporting mixed precision to gather dense matrix rows ([#901](#901)) + Add mixed precision SparsityCsr SpMV support ([#970](#970)) + Allow creating CSR submatrix including from (possibly discontinuous) index sets ([#885](#885), [#964](#964)) + Add a scaled identity addition (M <- aI + bM) feature interface and impls for Csr and Dense ([#942](#942)) Deprecations and important changes: + Deprecate AmgxPgm in favor of the new Pgm name. ([#1149](#1149)). + Deprecate specialized residual norm classes in favor of a common `ResidualNorm` class ([#1101](#1101)) + Deprecate CamelCase non-polymorphic types in favor of snake_case versions (like array, machine_topology, uninitialized_array, index_set) ([#1031](#1031), [#1052](#1052)) + Bug fix: restrict gko::share to rvalue references (*possible interface break*) ([#1020](#1020)) + Bug fix: when using cuSPARSE's triangular solvers, specifying the factory parameter `num_rhs` is now required when solving for more than one right-hand side, otherwise an exception is thrown ([#1184](#1184)). + Drop official support for old CUDA < 9.2 ([#887](#887)) Improved performance additions: + Reuse tmp storage in reductions in solvers and add a mutable workspace to all solvers ([#1013](#1013), [#1028](#1028)) + Add HIP unsafe atomic option for AMD ([#1091](#1091)) + Prefer vendor implementations for Dense dot, conj_dot and norm2 when available ([#967](#967)). + Tuned OpenMP SellP, COO, and ELL SpMV kernels for a small number of RHS ([#809](#809)) Fixes: + Fix various compilation warnings ([#1076](#1076), [#1183](#1183), [#1189](#1189)) + Fix issues with hwloc-related tests ([#1074](#1074)) + Fix include headers for GCC 12 ([#1071](#1071)) + Fix for simple-solver-logging example ([#1066](#1066)) + Fix for potential memory leak in Logger ([#1056](#1056)) + Fix logging of mixin classes ([#1037](#1037)) + Improve value semantics for LinOp types, like moved-from state in cross-executor copy/clones ([#753](#753)) + Fix some matrix SpMV and conversion corner cases ([#905](#905), [#978](#978)) + Fix uninitialized data ([#958](#958)) + Fix CUDA version requirement for cusparseSpSM ([#953](#953)) + Fix several issues within bash-script ([#1016](#1016)) + Fixes for `NVHPC` compiler support ([#1194](#1194)) Other additions: + Simplify and properly name GMRES kernels ([#861](#861)) + Improve pkg-config support for non-CMake libraries ([#923](#923), [#1109](#1109)) + Improve gdb pretty printer ([#987](#987), [#1114](#1114)) + Add a logger highlighting inefficient allocation and copy patterns ([#1035](#1035)) + Improved and optimized test random matrix generation ([#954](#954), [#1032](#1032)) + Better CSR strategy defaults ([#969](#969)) + Add `move_from` to `PolymorphicObject` ([#997](#997)) + Remove unnecessary device_guard usage ([#956](#956)) + Improvements to the generic accessor for mixed-precision ([#727](#727)) + Add a naive lower triangular solver implementation for CUDA ([#764](#764)) + Add support for int64 indices from CUDA 11 onward with SpMV and SpGEMM ([#897](#897)) + Add a L1 norm implementation ([#900](#900)) + Add reduce_add for arrays ([#831](#831)) + Add utility to simplify Dense View creation from an existing Dense vector ([#1136](#1136)). + Add a custom transpose implementation for Fbcsr and Csr transpose for unsupported vendor types ([#1123](#1123)) + Make IDR random initilization deterministic ([#1116](#1116)) + Move the algorithm choice for triangular solvers from Csr::strategy_type to a factory parameter ([#1088](#1088)) + Update CUDA archCoresPerSM ([#1175](#1116)) + Add kernels for Csr sparsity pattern lookup ([#994](#994)) + Differentiate between structural and numerical zeros in Ell/Sellp ([#1027](#1027)) + Add a binary IO format for matrix data ([#984](#984)) + Add a tuple zip_iterator implementation ([#966](#966)) + Simplify kernel stubs and declarations ([#888](#888)) + Simplify GKO_REGISTER_OPERATION with lambdas ([#859](#859)) + Simplify copy to device in tests and examples ([#863](#863)) + More verbose output to array assertions ([#858](#858)) + Allow parallel compilation for Jacobi kernels ([#871](#871)) + Change clang-format pointer alignment to left ([#872](#872)) + Various improvements and fixes to the benchmarking framework ([#750](#750), [#759](#759), [#870](#870), [#911](#911), [#1033](#1033), [#1137](#1137)) + Various documentation improvements ([#892](#892), [#921](#921), [#950](#950), [#977](#977), [#1021](#1021), [#1068](#1068), [#1069](#1069), [#1080](#1080), [#1081](#1081), [#1108](#1108), [#1153](#1153), [#1154](#1154)) + Various CI improvements ([#868](#868), [#874](#874), [#884](#884), [#889](#889), [#899](#899), [#903](#903), [#922](#922), [#925](#925), [#930](#930), [#936](#936), [#937](#937), [#958](#958), [#882](#882), [#1011](#1011), [#1015](#1015), [#989](#989), [#1039](#1039), [#1042](#1042), [#1067](#1067), [#1073](#1073), [#1075](#1075), [#1083](#1083), [#1084](#1084), [#1085](#1085), [#1139](#1139), [#1178](#1178), [#1187](#1187))

pratikvn added is:new-feature A request or implementation of a feature that does not exist yet. 1:ST:WIP This PR is a work in progress. Not ready for review. labels Feb 4, 2022

pratikvn added this to the Ginkgo 1.5.0 milestone Feb 4, 2022

pratikvn self-assigned this Feb 4, 2022

ginkgo-bot added mod:all This touches all Ginkgo modules. reg:testing This is related to testing. type:matrix-format This is related to the Matrix formats labels Feb 4, 2022

pratikvn force-pushed the submatrix-index-set branch from a942ad2 to 889a53a Compare February 15, 2022 17:21

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pratikvn mentioned this pull request Mar 4, 2022

Add a uniform coarsening algorithm for coarse grid generation. #979

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pratikvn requested a review from yhmtsai March 10, 2022 09:28

pratikvn force-pushed the submatrix-index-set branch from a690dba to 705d67e Compare March 10, 2022 13:02

pratikvn and others added 12 commits March 23, 2022 18:04

Fix for init_list space size detection

bb37854

Allow index gt index_space_size

9f90b74

Remove workaround and call kernels directly

851026a

Format files

12d694f

Co-authored-by: Pratik Nayak <[email protected]>

Parallelize omp by subsets

8d5e2eb

Review update.

a09f223

Co-authored-by: Yu-Hsiang Tsai <[email protected]> Co-authored-by: Tobias Ribizel <[email protected]>

Minimize allocs in reference kernel.

2efaf51

Add scoped_trace and fix omp kernel.

d69f7ea

Remove allocs inside loops

b0354a6

Review update.

2a3c062

Co-authored-by: Yuhsiang Tsai <[email protected]>

Some kernel perf updates.

841c827

Co-authored-by: Yuhsiang Tsai <[email protected]>

Review updates.

690b15b

Co-authored-by: Yu-Hsiang Tsai <[email protected]>

pratikvn force-pushed the submatrix-index-set branch from 7add1a0 to b716491 Compare March 23, 2022 20:52

Review update.

5fe2f23

Co-authored-by: Tobias Ribizel <[email protected]> Co-authored-by: Marcel Koch <[email protected]>

pratikvn force-pushed the submatrix-index-set branch from b716491 to 5fe2f23 Compare March 23, 2022 21:11

pratikvn added 1:ST:run-full-test 1:ST:ready-to-merge This PR is ready to merge. and removed 1:ST:ready-for-review This PR is ready for review labels Mar 23, 2022

pratikvn added 2 commits March 25, 2022 15:30

Make IndexSet a non-polymorphic object.

f4ffc36

Rename IndexSet to index_set

3982fe1

pratikvn requested a review from upsj March 27, 2022 10:07

upsj reviewed Mar 28, 2022

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include/ginkgo/core/base/index_set.hpp Show resolved Hide resolved

Add move and copy constr/assign ops.

7a8c7e6

upsj approved these changes Mar 29, 2022

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Review update.

43545a0

Co-authored-by: Tobias Ribizel<[email protected]>

pratikvn merged commit 6df4a68 into develop Mar 30, 2022

pratikvn deleted the submatrix-index-set branch March 30, 2022 08:57

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Create submatrix from Index sets #964

Create submatrix from Index sets #964

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Create submatrix from Index sets #964

Create submatrix from Index sets #964

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pratikvn commented Feb 4, 2022 • edited Loading

TODO

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