Add new accessor #643

thoasm · 2020-09-18T00:42:39Z

Add both reduced_row_major and scaled_reduced_row_major accessors to Ginkgo (naming is up for debate).

The tests should cover everything now, and the public interface remains unchanged.

It would also be nice if the function/operator range::operator= would be marked as deprecated since it is not optimized at all.
However, this will lead to a lot of deprecated warnings in our own code (mainly include/ginkgo/core/base/matrix_data.hpp and examples/ginkgo-ranges/ginkgo-ranges.cpp), so it should be done in another PR.

TODO:

Extend scaled_reduced_row_major tests
Add operator tests (*, ..., *=, ...)
~~Add constexpr tests for both~~ (not possible to create a constexpr accessor)
~~Add to_const() to range (and test it)~~ (This would change the interface; Workaround: use the accessor to_const() directly works fine).
Make core tests typed, so more combinations are tested
Adapt code to deal with dimensionalities other than 3
Test (and likely change) the behaviour of detail::enable_write_scalar in case the accessor is const. Likely simply add boolean with true for const, and false for non-const. Also, rename ScaleType to ScalarType.

codecov · 2020-09-22T12:12:41Z

Codecov Report

Merging #643 (07f6478) into develop (bf39bbe) will increase coverage by 0.12%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #643      +/-   ##
===========================================
+ Coverage    92.88%   93.01%   +0.12%     
===========================================
  Files          333      337       +4     
  Lines        24428    24876     +448     
===========================================
+ Hits         22691    23139     +448     
  Misses        1737     1737

Impacted Files	Coverage Δ
core/base/extended_float.hpp	`92.23% <ø> (+0.97%)`	⬆️
include/ginkgo/core/base/types.hpp	`92.59% <ø> (ø)`
core/base/accessor_helper.hpp	`100.00% <100.00%> (ø)`
core/base/accessor_references.hpp	`100.00% <100.00%> (ø)`
core/base/accessors.hpp	`100.00% <100.00%> (ø)`
core/test/base/accessors_reduced_storage.cpp	`100.00% <100.00%> (ø)`
core/test/base/dim.cpp	`100.00% <100.00%> (ø)`
core/test/base/range_accessors.cpp	`100.00% <100.00%> (ø)`
include/ginkgo/core/base/dim.hpp	`91.83% <100.00%> (+2.94%)`	⬆️
include/ginkgo/core/base/range_accessors.hpp	`73.68% <100.00%> (ø)`
... and 8 more

Continue to review full report at Codecov.

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pratikvn

Great work on this! Very nicely documented.

Some minor nits and questions. A few naming suggestions. A lot of spam about new lines.

core/test/base/range_accessors.cpp

include/ginkgo/core/base/range_accessors.hpp

include/ginkgo/core/base/types.hpp

core/test/base/range_accessors.cpp

tcojean

LGTM. Great work!

include/ginkgo/core/base/range_accessor_references.hpp

include/ginkgo/core/base/range_accessor_helper.hpp

include/ginkgo/core/base/range_accessors.hpp

tcojean · 2020-11-17T10:23:09Z

include/ginkgo/core/base/range_accessors.hpp

+     * @warning Do not use this function since it is not optimized for a
+     *          specific executor. It will always be performed sequentially.
+     *          Please write an optimized version (adjusted to the architecture)
+     *          by iterating through the values yourself.


It doesn't have to be part of the PR, but it would be nice to have an example on that topic at some point, I think.

include/ginkgo/core/base/range_accessors.hpp

core/test/base/range_accessors.cpp

tcojean · 2020-11-17T10:44:14Z

On the issue pointed by sonarcloud, maybe indeed you should use Args... &&args in some places?

tcojean · 2020-11-17T13:17:22Z

Another sonarqube related comment, I think it's possible to remove quite a bit of the "code smells" left, a lot of them amount to:

there is no need to add inline to a constexpr function (it's already necessarily inlined)
sometimes you declare the parameter name size but don't use it, removing the parameter name will remove this kind of warning

thoasm · 2020-11-17T14:05:14Z

@tcojean I haven't actually looked too much into the sonarcloud Smells yet, thanks for pointing that out.
Do you know if the implicitly declared inline is as strong as the __forceinline__ from CUDA?

Removing the name of the parameter was something I also did in the latest commit (I fixed perfect forwarding and unused parameters). I will look into the other smells today.

thoasm

Replies addressing @tcojean 's comments.

include/ginkgo/core/base/range_accessor_references.hpp

include/ginkgo/core/base/range_accessor_helper.hpp

include/ginkgo/core/base/range_accessor_references.hpp

core/test/base/range_accessors.cpp

- explicitly state what variables to capture in a lambda - add `explicit` to reference_class constructors - add `noexcept` for reference_class copy move assignment

Additionally, fix minor code smells

Use `std::numeric_limits<>::epsilon()` for the test reduction factor

Co-authored-by: Thomas Grützmacher <thoasm@users.noreply.github.com>

Previously, a write_scalar function always existed, even though the scalar value was const, therefore not writable. Now, the write_scalar function only exists for the proper non-const accessor.

thoasm · 2021-01-13T04:19:15Z

format!

Co-authored-by: Thomas Grützmacher <thoasm@users.noreply.github.com>

Make a distinction between addressing the scalar value with the direct indices (specifying the actual indices without the ignored ones) and with masked indices (specifying all dimensions while ignoring all where the bit of the scalar mask is not set). Read and write functions are available for both variants.

core/test/base/dim.cpp

include/ginkgo/core/base/dim.hpp

pratikvn

Only some very minor nits. LGTM!

core/base/accessor_references.hpp

core/base/accessor_helper.hpp

Co-authored-by: Pratik Nayak <pratikvn@protonmail.com>

upsj

LGTM! Nice job, especially juggling all the templates 😄

core/base/extended_float.hpp

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

sonarcloud · 2021-01-22T03:33:14Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

100.0% Coverage
2.9% Duplication

Ginkgo release 1.4.0 The Ginkgo team is proud to announce the new Ginkgo minor release 1.4.0. This release brings most of the Ginkgo functionality to the Intel DPC++ ecosystem which enables Intel-GPU and CPU execution. The only Ginkgo features which have not been ported yet are some preconditioners. Ginkgo's mixed-precision support is greatly enhanced thanks to: 1. The new Accessor concept, which allows writing kernels featuring on-the-fly memory compression, among other features. The accessor can be used as header-only, see the [accessor BLAS benchmarks repository](https://github.com/ginkgo-project/accessor-BLAS/tree/develop) as a usage example. 2. All LinOps now transparently support mixed-precision execution. By default, this is done through a temporary copy which may have a performance impact but already allows mixed-precision research. Native mixed-precision ELL kernels are implemented which do not see this cost. The accessor is also leveraged in a new CB-GMRES solver which allows for performance improvements by compressing the Krylov basis vectors. Many other features have been added to Ginkgo, such as reordering support, a new IDR solver, Incomplete Cholesky preconditioner, matrix assembly support (only CPU for now), machine topology information, and more! Supported systems and requirements: + For all platforms, cmake 3.13+ + C++14 compliant compiler + Linux and MacOS + gcc: 5.3+, 6.3+, 7.3+, all versions after 8.1+ + clang: 3.9+ + Intel compiler: 2018+ + Apple LLVM: 8.0+ + CUDA module: CUDA 9.0+ + HIP module: ROCm 3.5+ + DPC++ module: Intel OneAPI 2021.3. Set the CXX compiler to `dpcpp`. + Windows + MinGW and Cygwin: gcc 5.3+, 6.3+, 7.3+, all versions after 8.1+ + Microsoft Visual Studio: VS 2019 + CUDA module: CUDA 9.0+, Microsoft Visual Studio + OpenMP module: MinGW or Cygwin. Algorithm and important feature additions: + Add a new DPC++ Executor for SYCL execution and other base utilities [#648](#648), [#661](#661), [#757](#757), [#832](#832) + Port matrix formats, solvers and related kernels to DPC++. For some kernels, also make use of a shared kernel implementation for all executors (except Reference). [#710](#710), [#799](#799), [#779](#779), [#733](#733), [#844](#844), [#843](#843), [#789](#789), [#845](#845), [#849](#849), [#855](#855), [#856](#856) + Add accessors which allow multi-precision kernels, among other things. [#643](#643), [#708](#708) + Add support for mixed precision operations through apply in all LinOps. [#677](#677) + Add incomplete Cholesky factorizations and preconditioners as well as some improvements to ILU. [#672](#672), [#837](#837), [#846](#846) + Add an AMGX implementation and kernels on all devices but DPC++. [#528](#528), [#695](#695), [#860](#860) + Add a new mixed-precision capability solver, Compressed Basis GMRES (CB-GMRES). [#693](#693), [#763](#763) + Add the IDR(s) solver. [#620](#620) + Add a new fixed-size block CSR matrix format (for the Reference executor). [#671](#671), [#730](#730) + Add native mixed-precision support to the ELL format. [#717](#717), [#780](#780) + Add Reverse Cuthill-McKee reordering [#500](#500), [#649](#649) + Add matrix assembly support on CPUs. [#644](#644) + Extends ISAI from triangular to general and spd matrices. [#690](#690) Other additions: + Add the possibility to apply real matrices to complex vectors. [#655](#655), [#658](#658) + Add functions to compute the absolute of a matrix format. [#636](#636) + Add symmetric permutation and improve existing permutations. [#684](#684), [#657](#657), [#663](#663) + Add a MachineTopology class with HWLOC support [#554](#554), [#697](#697) + Add an implicit residual norm criterion. [#702](#702), [#818](#818), [#850](#850) + Row-major accessor is generalized to more than 2 dimensions and a new "block column-major" accessor has been added. [#707](#707) + Add an heat equation example. [#698](#698), [#706](#706) + Add ccache support in CMake and CI. [#725](#725), [#739](#739) + Allow tuning and benchmarking variables non intrusively. [#692](#692) + Add triangular solver benchmark [#664](#664) + Add benchmarks for BLAS operations [#772](#772), [#829](#829) + Add support for different precisions and consistent index types in benchmarks. [#675](#675), [#828](#828) + Add a Github bot system to facilitate development and PR management. [#667](#667), [#674](#674), [#689](#689), [#853](#853) + Add Intel (DPC++) CI support and enable CI on HPC systems. [#736](#736), [#751](#751), [#781](#781) + Add ssh debugging for Github Actions CI. [#749](#749) + Add pipeline segmentation for better CI speed. [#737](#737) Changes: + Add a Scalar Jacobi specialization and kernels. [#808](#808), [#834](#834), [#854](#854) + Add implicit residual log for solvers and benchmarks. [#714](#714) + Change handling of the conjugate in the dense dot product. [#755](#755) + Improved Dense stride handling. [#774](#774) + Multiple improvements to the OpenMP kernels performance, including COO, an exclusive prefix sum, and more. [#703](#703), [#765](#765), [#740](#740) + Allow specialization of submatrix and other dense creation functions in solvers. [#718](#718) + Improved Identity constructor and treatment of rectangular matrices. [#646](#646) + Allow CUDA/HIP executors to select allocation mode. [#758](#758) + Check if executors share the same memory. [#670](#670) + Improve test install and smoke testing support. [#721](#721) + Update the JOSS paper citation and add publications in the documentation. [#629](#629), [#724](#724) + Improve the version output. [#806](#806) + Add some utilities for dim and span. [#821](#821) + Improved solver and preconditioner benchmarks. [#660](#660) + Improve benchmark timing and output. [#669](#669), [#791](#791), [#801](#801), [#812](#812) Fixes: + Sorting fix for the Jacobi preconditioner. [#659](#659) + Also log the first residual norm in CGS [#735](#735) + Fix BiCG and HIP CSR to work with complex matrices. [#651](#651) + Fix Coo SpMV on strided vectors. [#807](#807) + Fix segfault of extract_diagonal, add short-and-fat test. [#769](#769) + Fix device_reset issue by moving counter/mutex to device. [#810](#810) + Fix `EnableLogging` superclass. [#841](#841) + Support ROCm 4.1.x and breaking HIP_PLATFORM changes. [#726](#726) + Decreased test size for a few device tests. [#742](#742) + Fix multiple issues with our CMake HIP and RPATH setup. [#712](#712), [#745](#745), [#709](#709) + Cleanup our CMake installation step. [#713](#713) + Various simplification and fixes to the Windows CMake setup. [#720](#720), [#785](#785) + Simplify third-party integration. [#786](#786) + Improve Ginkgo device arch flags management. [#696](#696) + Other fixes and improvements to the CMake setup. [#685](#685), [#792](#792), [#705](#705), [#836](#836) + Clarification of dense norm documentation [#784](#784) + Various development tools fixes and improvements [#738](#738), [#830](#830), [#840](#840) + Make multiple operators/constructors explicit. [#650](#650), [#761](#761) + Fix some issues, memory leaks and warnings found by MSVC. [#666](#666), [#731](#731) + Improved solver memory estimates and consistent iteration counts [#691](#691) + Various logger improvements and fixes [#728](#728), [#743](#743), [#754](#754) + Fix for ForwardIterator requirements in iterator_factory. [#665](#665) + Various benchmark fixes. [#647](#647), [#673](#673), [#722](#722) + Various CI fixes and improvements. [#642](#642), [#641](#641), [#795](#795), [#783](#783), [#793](#793), [#852](#852) Related PR: #857

Release 1.4.0 to master The Ginkgo team is proud to announce the new Ginkgo minor release 1.4.0. This release brings most of the Ginkgo functionality to the Intel DPC++ ecosystem which enables Intel-GPU and CPU execution. The only Ginkgo features which have not been ported yet are some preconditioners. Ginkgo's mixed-precision support is greatly enhanced thanks to: 1. The new Accessor concept, which allows writing kernels featuring on-the-fly memory compression, among other features. The accessor can be used as header-only, see the [accessor BLAS benchmarks repository](https://github.com/ginkgo-project/accessor-BLAS/tree/develop) as a usage example. 2. All LinOps now transparently support mixed-precision execution. By default, this is done through a temporary copy which may have a performance impact but already allows mixed-precision research. Native mixed-precision ELL kernels are implemented which do not see this cost. The accessor is also leveraged in a new CB-GMRES solver which allows for performance improvements by compressing the Krylov basis vectors. Many other features have been added to Ginkgo, such as reordering support, a new IDR solver, Incomplete Cholesky preconditioner, matrix assembly support (only CPU for now), machine topology information, and more! Supported systems and requirements: + For all platforms, cmake 3.13+ + C++14 compliant compiler + Linux and MacOS + gcc: 5.3+, 6.3+, 7.3+, all versions after 8.1+ + clang: 3.9+ + Intel compiler: 2018+ + Apple LLVM: 8.0+ + CUDA module: CUDA 9.0+ + HIP module: ROCm 3.5+ + DPC++ module: Intel OneAPI 2021.3. Set the CXX compiler to `dpcpp`. + Windows + MinGW and Cygwin: gcc 5.3+, 6.3+, 7.3+, all versions after 8.1+ + Microsoft Visual Studio: VS 2019 + CUDA module: CUDA 9.0+, Microsoft Visual Studio + OpenMP module: MinGW or Cygwin. Algorithm and important feature additions: + Add a new DPC++ Executor for SYCL execution and other base utilities [#648](#648), [#661](#661), [#757](#757), [#832](#832) + Port matrix formats, solvers and related kernels to DPC++. For some kernels, also make use of a shared kernel implementation for all executors (except Reference). [#710](#710), [#799](#799), [#779](#779), [#733](#733), [#844](#844), [#843](#843), [#789](#789), [#845](#845), [#849](#849), [#855](#855), [#856](#856) + Add accessors which allow multi-precision kernels, among other things. [#643](#643), [#708](#708) + Add support for mixed precision operations through apply in all LinOps. [#677](#677) + Add incomplete Cholesky factorizations and preconditioners as well as some improvements to ILU. [#672](#672), [#837](#837), [#846](#846) + Add an AMGX implementation and kernels on all devices but DPC++. [#528](#528), [#695](#695), [#860](#860) + Add a new mixed-precision capability solver, Compressed Basis GMRES (CB-GMRES). [#693](#693), [#763](#763) + Add the IDR(s) solver. [#620](#620) + Add a new fixed-size block CSR matrix format (for the Reference executor). [#671](#671), [#730](#730) + Add native mixed-precision support to the ELL format. [#717](#717), [#780](#780) + Add Reverse Cuthill-McKee reordering [#500](#500), [#649](#649) + Add matrix assembly support on CPUs. [#644](#644) + Extends ISAI from triangular to general and spd matrices. [#690](#690) Other additions: + Add the possibility to apply real matrices to complex vectors. [#655](#655), [#658](#658) + Add functions to compute the absolute of a matrix format. [#636](#636) + Add symmetric permutation and improve existing permutations. [#684](#684), [#657](#657), [#663](#663) + Add a MachineTopology class with HWLOC support [#554](#554), [#697](#697) + Add an implicit residual norm criterion. [#702](#702), [#818](#818), [#850](#850) + Row-major accessor is generalized to more than 2 dimensions and a new "block column-major" accessor has been added. [#707](#707) + Add an heat equation example. [#698](#698), [#706](#706) + Add ccache support in CMake and CI. [#725](#725), [#739](#739) + Allow tuning and benchmarking variables non intrusively. [#692](#692) + Add triangular solver benchmark [#664](#664) + Add benchmarks for BLAS operations [#772](#772), [#829](#829) + Add support for different precisions and consistent index types in benchmarks. [#675](#675), [#828](#828) + Add a Github bot system to facilitate development and PR management. [#667](#667), [#674](#674), [#689](#689), [#853](#853) + Add Intel (DPC++) CI support and enable CI on HPC systems. [#736](#736), [#751](#751), [#781](#781) + Add ssh debugging for Github Actions CI. [#749](#749) + Add pipeline segmentation for better CI speed. [#737](#737) Changes: + Add a Scalar Jacobi specialization and kernels. [#808](#808), [#834](#834), [#854](#854) + Add implicit residual log for solvers and benchmarks. [#714](#714) + Change handling of the conjugate in the dense dot product. [#755](#755) + Improved Dense stride handling. [#774](#774) + Multiple improvements to the OpenMP kernels performance, including COO, an exclusive prefix sum, and more. [#703](#703), [#765](#765), [#740](#740) + Allow specialization of submatrix and other dense creation functions in solvers. [#718](#718) + Improved Identity constructor and treatment of rectangular matrices. [#646](#646) + Allow CUDA/HIP executors to select allocation mode. [#758](#758) + Check if executors share the same memory. [#670](#670) + Improve test install and smoke testing support. [#721](#721) + Update the JOSS paper citation and add publications in the documentation. [#629](#629), [#724](#724) + Improve the version output. [#806](#806) + Add some utilities for dim and span. [#821](#821) + Improved solver and preconditioner benchmarks. [#660](#660) + Improve benchmark timing and output. [#669](#669), [#791](#791), [#801](#801), [#812](#812) Fixes: + Sorting fix for the Jacobi preconditioner. [#659](#659) + Also log the first residual norm in CGS [#735](#735) + Fix BiCG and HIP CSR to work with complex matrices. [#651](#651) + Fix Coo SpMV on strided vectors. [#807](#807) + Fix segfault of extract_diagonal, add short-and-fat test. [#769](#769) + Fix device_reset issue by moving counter/mutex to device. [#810](#810) + Fix `EnableLogging` superclass. [#841](#841) + Support ROCm 4.1.x and breaking HIP_PLATFORM changes. [#726](#726) + Decreased test size for a few device tests. [#742](#742) + Fix multiple issues with our CMake HIP and RPATH setup. [#712](#712), [#745](#745), [#709](#709) + Cleanup our CMake installation step. [#713](#713) + Various simplification and fixes to the Windows CMake setup. [#720](#720), [#785](#785) + Simplify third-party integration. [#786](#786) + Improve Ginkgo device arch flags management. [#696](#696) + Other fixes and improvements to the CMake setup. [#685](#685), [#792](#792), [#705](#705), [#836](#836) + Clarification of dense norm documentation [#784](#784) + Various development tools fixes and improvements [#738](#738), [#830](#830), [#840](#840) + Make multiple operators/constructors explicit. [#650](#650), [#761](#761) + Fix some issues, memory leaks and warnings found by MSVC. [#666](#666), [#731](#731) + Improved solver memory estimates and consistent iteration counts [#691](#691) + Various logger improvements and fixes [#728](#728), [#743](#743), [#754](#754) + Fix for ForwardIterator requirements in iterator_factory. [#665](#665) + Various benchmark fixes. [#647](#647), [#673](#673), [#722](#722) + Various CI fixes and improvements. [#642](#642), [#641](#641), [#795](#795), [#783](#783), [#793](#793), [#852](#852) Related PR: #866

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Mixed Precision Gmres #640

Closed

2 tasks

Thomas Grützmacher and others added 12 commits January 13, 2021 04:49

Only use forwarding references when forwarding

1539c47

Fix more sonarcloud code smells

722f42a

- explicitly state what variables to capture in a lambda - add `explicit` to reference_class constructors - add `noexcept` for reference_class copy move assignment

Fix OMP Jacobi test error

c57b13d

Add gko::half to the accessor testing

9ffba01

Additionally, fix minor code smells

Specify return type of reference operators again

5aa794d

Move new accessor to private headers

941a287

Add numeric_limits to gko::half

0aa9bb3

Use `std::numeric_limits<>::epsilon()` for the test reduction factor

Move compute_default_stride_array to dim header

b7816e9

Move are_all_integral to types.hpp

de70976

Format files

a599ddd

Co-authored-by: Thomas Grützmacher <thoasm@users.noreply.github.com>

Only add write scalar option when non-const

980ac87

Previously, a write_scalar function always existed, even though the scalar value was const, therefore not writable. Now, the write_scalar function only exists for the proper non-const accessor.

Include complex numbers in accessor tests

fcddab6

thoasm force-pushed the add_new_accessor branch from d4ca8cb to fcddab6 Compare January 13, 2021 04:11

ginkgo-bot and others added 2 commits January 13, 2021 04:20

Format files

c6e80a0

Co-authored-by: Thomas Grützmacher <thoasm@users.noreply.github.com>

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Review update

07f6478

Co-authored-by: Tobias Ribizel <ribizel@kit.edu>

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Add Compressed Basis GMRES (CB-GMRES) #693

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