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Scaling + addition by scaled identity (M <- aI + bM) for Csr and Dense matrices #942

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merged 22 commits into from
Feb 19, 2022
Merged

Scaling + addition by scaled identity (M <- aI + bM) for Csr and Dense matrices #942

merged 22 commits into from
Feb 19, 2022

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Slaedr
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@Slaedr Slaedr commented Dec 20, 2021 •
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Enables M <- a I + b M operations when M is Dense or Csr. These are optimized kernels that can be used for:

  • assembling the LHS for a backward Euler type time integration of a PDE
  • shifting a matrix before precondition construction, eg. for nearly singular problems.

In addition, there's a small bugfix to the 2D common kernel run function. Now, the constness of the pointer to the matrix does not determine whether the entries can be modified; earlier something like Mtx* const mtx would not allow the matrix to be modified in the kernel.

@ginkgo-bot ginkgo-bot added mod:all This touches all Ginkgo modules. reg:build This is related to the build system. reg:testing This is related to testing. type:matrix-format This is related to the Matrix formats labels Dec 20, 2021
@Slaedr Slaedr added the 1:ST:ready-for-review This PR is ready for review label Dec 20, 2021
pratikvn
pratikvn approved these changes Dec 21, 2021
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Nice work. Thanks for adding this so quickly! Mostly minor things. But otherwise looks good!

@pratikvn pratikvn added this to the Ginkgo 1.5.0 milestone Dec 21, 2021
@Slaedr Slaedr removed their assignment Dec 21, 2021
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codecov bot commented Dec 21, 2021 •
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Codecov Report

Merging #942 (6b65cb4) into develop (fc6322b) will increase coverage by 0.16%.
The diff coverage is 97.17%.

❗ Current head 6b65cb4 differs from pull request most recent head 534d1b8. Consider uploading reports for the commit 534d1b8 to get more accurate results

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #942      +/-   ##
===========================================
+ Coverage    92.17%   92.34%   +0.16%     
===========================================
  Files          479      480       +1     
  Lines        39673    39925     +252     
===========================================
+ Hits         36570    36867     +297     
+ Misses        3103     3058      -45
Impacted Files Coverage Δ
core/device_hooks/common_kernels.inc.cpp 0.00% <0.00%> (ø)
core/test/utils.hpp 100.00% <ø> (ø)
include/ginkgo/core/base/exception_helpers.hpp 90.90% <ø> (ø)
include/ginkgo/core/matrix/csr.hpp 45.53% <ø> (ø)
include/ginkgo/core/matrix/dense.hpp 96.32% <ø> (ø)
omp/test/preconditioner/jacobi_kernels.cpp 100.00% <ø> (ø)
test/multigrid/amgx_pgm_kernels.cpp 100.00% <ø> (ø)
test/solver/bicg_kernels.cpp 98.37% <ø> (ø)
test/solver/bicgstab_kernels.cpp 100.00% <ø> (ø)
test/solver/cg_kernels.cpp 100.00% <ø> (ø)
... and 29 more

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@Slaedr Slaedr removed the 1:ST:ready-for-review This PR is ready for review label Dec 23, 2021
@Slaedr Slaedr self-assigned this Dec 23, 2021
@upsj upsj mentioned this pull request Jan 3, 2022
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@Slaedr Slaedr force-pushed the backward-euler-op branch from 771a5e4 to 9206e8f Compare January 5, 2022 22:10
@Slaedr Slaedr removed their assignment Jan 5, 2022
@Slaedr Slaedr added the 1:ST:ready-for-review This PR is ready for review label Jan 5, 2022
pratikvn
pratikvn previously requested changes Jan 6, 2022
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I think the tests should be moved to backend/test/matrix/'csr/dense'_kernels.cpp instead of Identity as this currently does not do anything with the Identity interface. Then you can delete all the identity test files as well.

Otherwise looks good to me.

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Slaedr commented Jan 6, 2022 •
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@pratikvn Since we are making the operation available via Identity's advanced apply as well, I think we should have a test for that. That would then automatically also test the mixin interface.

The Identity advanced apply does not support rectangular matrices, so that case is tested separately for the mixin interface.

@Slaedr Slaedr force-pushed the backward-euler-op branch from 9206e8f to a990e91 Compare January 10, 2022 16:47
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The reason I would prefer the tests in the kernel tests is because the kernels themselves are in the Dense and CSR classes. Identity is just using those kernels. So IMO, they should be tested where they are implemented, which here is the classes themselves. Additionally, then you can just call the actual kernels, add_scaled_identity, which I feel is more clear than just directly calling the apply in the Identity class.

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Slaedr commented Jan 11, 2022

@pratikvn For now, rectangular matrices are being tested for the respective matrix types using add_scaled_identity only in reference, not the other backends. Square matrices are being tested for all backends under identity. I think I will leave the identity tests as they are, and add rectangular tests for all backends under the respective matrix types using add_scaled_identity. That should test both interfaces adequately.

@Slaedr Slaedr self-assigned this Jan 11, 2022
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Okay, I guess that is fine.

Slaedr and others added 21 commits February 17, 2022 19:58
@Slaedr
enabled the operation A <- a I + b A for dense A in Identity advanced…
31c8583 
… apply
@Slaedr
added A <- aI + bA for A CSR in identity advanced apply
6a31e99
@Slaedr
Dpcpp and hip fixes, and removed unused code from review
25bbef7
@Slaedr
fixed typos in hip kernel
4ce6ef6
@Slaedr @pratikvn
review comments on tolerances
7c08acd 
Co-authored-by: Pratik Nayak <pratikvn@protonmail.com>
@Slaedr
refactored code to add scaled identity, introduced new mixin
84d504e
@Slaedr
streamlined tests for scaled identity addition operation
acfe896 
The strategy is:
- The operation on non-square matrices is tested in the respective
matrix test suite.
- That on square matrices is tested in the identity test suite.
@Slaedr
added separate feature class and mixin for scaled identity addition
bef65f8
@Slaedr
added kernels to detect zero diagonals and related exception
390867d
@Slaedr
removed identity common tests, moved csr add_scaled_identity tests to…
a82d2a2 
… backend-specific files
@Slaedr
removed Identity interface to add_scaled_identity, fixed hip issues
a02f4f5
@Slaedr
removed unnecessary includes and completed omp tests
001a7ca
@Slaedr
replaced as with static_cast in mixin
4abf655
@Slaedr @upsj
Review comments
a995ed6 
Changed signature of check_diagonal_entries_exist kernel
Added checks for zero-range kernel launches for cuda and hip.

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
@Slaedr @upsj
review comments
bea2f7e 
Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
@Slaedr @upsj
Simplified test utils; add_scaled_identity now uses temporary convers…
1046c98 
…ions.

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
@Slaedr @upsj
Simpler algorithm for diagonal check
c9323a2 
Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
@Slaedr
fixed issue with circular header check
3b3b357
@Slaedr @upsj
review comments - fix zero kernel launch
e7f1fd1 
Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
@Slaedr @yhmtsai
Simplified ScaledIdentityAddable interface
b861825 
The ConcreteType was only needed for the executor. We now use LinOp for
that.

Co-authored-by: Yuhsiang M. Tsai <yhmtsai@gmail.com>
@Slaedr @upsj
Some simplifications from review comments
534d1b8 
Co-authored-by: Tobias Ribizel <ribizel@kit.edu>
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Note: This PR changes the Ginkgo ABI:

Functions changes summary: 0 Removed, 1383 Changed (17196 filtered out), 21 Added functions
Variables changes summary: 0 Removed, 0 Changed, 0 Added variable

For details check the full ABI diff under Artifacts here

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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 13 Code Smells

70.1% 70.1% Coverage
0.0% 0.0% Duplication

@Slaedr Slaedr added 1:ST:ready-to-merge This PR is ready to merge. 1:ST:run-full-test and removed 1:ST:ready-for-review This PR is ready for review labels Feb 18, 2022
@Slaedr Slaedr merged commit 6ee7bfe into develop Feb 19, 2022
@Slaedr Slaedr deleted the backward-euler-op branch February 19, 2022 08:09
tcojean added a commit that referenced this pull request Nov 12, 2022
@tcojean
Merge Release 1.5.0 to develop
7c9f530 
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))
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