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Add github bot #667

Merged
merged 3 commits into from
Nov 30, 2020
Merged

Add github bot #667

merged 3 commits into from
Nov 30, 2020

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@upsj upsj commented Nov 20, 2020

This PR adds a Github Action-based bot to the Ginkgo repository.
You can test it out at https://github.com/upsj/ginkgo-bot-playground

By default, it does the following actions:

  • On new PR by OWNER, COLLABORATOR or MEMBER: check which files have been changed and add appropriate labels (label.sh). The same check happens if an authorized user comments with label! on the PR
  • On new PR and sync (roughly after each push, if there are no merge conflicts to the base branch): check if any files need to be formatted (check-format.sh). The same check happens on a check-format! comment by an authorized user
  • On format! command from an authorized user, push a commit with the changes found by check-format! (format.sh)
  • On rebase!, rebase the current branch onto develop (rebase.sh)

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tcojean commented Nov 20, 2020

Probably to make it work I would need to do some setup in terms of Github variables settings and token, right?

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upsj commented Nov 20, 2020

@tcojean as far as I know, we don't need to setup anything, the actions are executed automatically

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upsj commented Nov 21, 2020

@pratikvn This won't work until the PR is merged, since issue_comment events are only dispatched to the default branch's workflows. You can test on my clone though, I just need to add you to the collaborator list :)

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Yes, I realized that after I commented. :)

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Nice! LGTM.

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sonarcloud bot commented Nov 24, 2020

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities (and Security Hotspot 0 Security Hotspots to review)
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

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codecov bot commented Nov 24, 2020

Codecov Report

Merging #667 (81755d7) into develop (b3c3596) will decrease coverage by 0.18%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #667      +/-   ##
===========================================
- Coverage    93.03%   92.84%   -0.19%     
===========================================
  Files          332      325       -7     
  Lines        24186    23296     -890     
===========================================
- Hits         22501    21630     -871     
+ Misses        1685     1666      -19     
Impacted Files Coverage Δ
include/ginkgo/core/base/range_accessors.hpp 73.68% <0.00%> (-5.27%) ⬇️
omp/reorder/rcm_kernels.cpp 94.44% <0.00%> (-3.70%) ⬇️
core/device_hooks/hip_hooks.cpp 51.72% <0.00%> (-3.12%) ⬇️
core/device_hooks/cuda_hooks.cpp 51.72% <0.00%> (-3.12%) ⬇️
core/stop/residual_norm.cpp 94.73% <0.00%> (-0.72%) ⬇️
omp/matrix/dense_kernels.cpp 97.56% <0.00%> (-0.61%) ⬇️
core/test/base/exception.cpp 100.00% <0.00%> (ø)
omp/test/solver/gmres_kernels.cpp 100.00% <0.00%> (ø)
core/test/base/exception_helpers.cpp 100.00% <0.00%> (ø)
include/ginkgo/core/base/exception.hpp 100.00% <0.00%> (ø)
... and 10 more

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LGTM. Some minor comments.

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@upsj upsj added the reg:ci-cd This is related to the continuous integration system. label Nov 27, 2020
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LGTM!

@upsj upsj added the 1:ST:ready-to-merge This PR is ready to merge. label Nov 27, 2020
@upsj upsj added 1:ST:ready-for-review This PR is ready for review and removed 1:ST:ready-to-merge This PR is ready to merge. labels Nov 27, 2020
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upsj commented Nov 27, 2020

I finished my changes, I would appreciate if you could take another look at it:

  • Unify check-format and format formatting step
  • Only format changed files
  • Upload a patch file after a failed check-format run
  • Incorporate format_header.sh and avoid header name collisions by adding PUBLIC_ to public header file include guards
  • Improve error output by linking to the failing Github Action.
  • Improve security by avoiding executing bash scripts that may be overwritten by a checkout while they are running

@upsj upsj removed the 1:ST:ready-for-review This PR is ready for review label Nov 30, 2020
@upsj upsj added the 1:ST:ready-to-merge This PR is ready to merge. label Nov 30, 2020
@upsj upsj merged commit 1cbdc8b into develop Nov 30, 2020
@upsj upsj deleted the add_github_bot branch November 30, 2020 11:21
tcojean added a commit that referenced this pull request Aug 20, 2021
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
tcojean added a commit that referenced this pull request Aug 23, 2021
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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