Format everything & delete old bot comments #674

upsj · 2020-12-02T12:28:44Z

This PR formats all files and fixes a few broken formatting configs, as well as deleting old comments from check-format! and rebase!

github-actions · 2020-12-02T12:30:01Z

Error: The following files need to be formatted:

core/preconditioner/jacobi_utils.hpp
core/test/base/executor.cpp
core/test/utils/matrix_generator.hpp
include/ginkgo/core/base/abstract_factory.hpp
include/ginkgo/core/base/combination.hpp
include/ginkgo/core/base/composition.hpp
include/ginkgo/core/base/dim.hpp
include/ginkgo/core/base/executor.hpp
include/ginkgo/core/base/lin_op.hpp
include/ginkgo/core/base/mtx_io.hpp
include/ginkgo/core/base/polymorphic_object.hpp
include/ginkgo/core/base/range.hpp
include/ginkgo/core/factorization/ilu.hpp
include/ginkgo/core/factorization/par_ict.hpp
include/ginkgo/core/factorization/par_ilu.hpp
include/ginkgo/core/factorization/par_ilut.hpp
include/ginkgo/core/log/logger.hpp
include/ginkgo/core/matrix/dense.hpp
include/ginkgo/core/matrix/sellp.hpp
include/ginkgo/core/preconditioner/jacobi.hpp

You can find a formatting patch under Artifacts here or run format! if you have write access to Ginkgo

upsj · 2020-12-02T12:31:45Z

Okay, that was an interesting fail 😆 I must have used the wrong clang-format version in format_header.sh

upsj · 2020-12-02T12:32:00Z

format!

pratikvn · 2020-12-02T12:57:07Z

So it also seems that format! comment does not trigger any CI pipelines ?

upsj · 2020-12-02T12:59:32Z

Yes, that seems to be a Github ~~bug~~ feature, where pushes by Actions don't cause push events to be triggered.

upsj · 2020-12-02T13:00:55Z

Related forum post: https://github.community/t/push-from-action-does-not-trigger-subsequent-action/16854
https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#triggering-new-workflows-using-a-personal-access-token

tcojean

LGTM.

.github/bot-pr-base.sh

reference/test/preconditioner/isai_kernels.cpp

pratikvn · 2020-12-02T17:25:13Z

But I think the bug would mean that whenever a format commit is added atleast the actions would need to be triggered right ? Can we do that manually ? Maybe you can add a command (like run-pipelines!) to trigger the pipelines instead ?

upsj · 2020-12-02T17:40:03Z

I am working on a workaround using a private access token, that should be simpler. In the future, I would probably add a check-pr! command to trigger Gitlab pipelines for PRs from forks.

github-actions · 2020-12-02T18:37:47Z

No formatting necessary

github-actions · 2020-12-02T18:54:11Z

No formatting necessary

pratikvn

LGTM! Only some minor things.

pratikvn · 2020-12-02T20:57:24Z

cuda/factorization/par_ilut_approx_filter_kernel.cu

@@ -44,7 +44,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


 #include "core/components/prefix_sum.hpp"
-#include "core/factorization/par_ilut_kernels.hpp"


Is this maybe necessary ?

I was as surprised as you are: This is a duplicate of the topmost header

pratikvn · 2020-12-02T21:02:54Z

omp/solver/idr_kernels.cpp

 #include <algorithm>
 #include <iostream>
 #include <random>
+#include <time.h>


Maybe this should be in a separate section of its own as it is a C header ?

I guess the correct include here would be ctime, which should definitely be part of the same group, or even use std::random_device, but I wanted to keep the changes as minimal as possible. Maybe something for a later PR?

pratikvn · 2020-12-02T21:03:34Z

omp/test/solver/idr_kernels.cpp

+#include <ginkgo/core/solver/bicgstab.hpp>
+#include <ginkgo/core/solver/gmres.hpp>
 #include <ginkgo/core/stop/combined.hpp>


Maybe these headers are not needed

pratikvn · 2020-12-02T21:04:16Z

reference/solver/idr_kernels.cpp

 #include <algorithm>
 #include <iostream>
 #include <random>
+#include <time.h>


Again, maybe better in its own section

yhmtsai

LGTM

yhmtsai · 2020-12-02T21:17:03Z

dev_tools/scripts/config

+- "core/test/base/allocator"
+ - FixInclude: "core/base/allocator.hpp"
+- "reference/test/base/utils"
+ - FixInclude: "core/base/utils.hpp"


at some point, I will check whether adding a special comment as the main header.

#include "core/base/utils.hpp" // MAIN

it will use it as main header no matter how the config sets

yhmtsai · 2020-12-02T21:20:58Z

test_install/test_install.cpp

+ auto abs_res =
+ gko::stop::AbsoluteResidualNorm<>::build().with_tolerance(1e-10).on(
+ refExec);


It seems to be formatted not well, but my local formatted result is the same as it

I wonder why this was reformatted like this. The existing code is actually easier to read and looks better.

Yes, this is pretty unfortunate. Luckily, this is only part of our install test, which we only rarely need to modify anyways.

Yes, when reviewing this I also thought the previous version looked better, but that's the usual clang-format shenanigans.

sonarcloud · 2020-12-03T09:31:57Z

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

100.0% Coverage
3.3% Duplication

codecov · 2020-12-03T09:52:11Z

Codecov Report

Merging #674 (562f290) into develop (1cbdc8b) will decrease coverage by 0.00%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #674      +/-   ##
===========================================
- Coverage    93.02%   93.02%   -0.01%     
===========================================
  Files          332      332              
  Lines        24187    24186       -1     
===========================================
- Hits         22500    22499       -1     
  Misses        1687     1687

Impacted Files	Coverage Δ
core/base/allocator.hpp	`100.00% <ø> (ø)`
core/base/utils.hpp	`100.00% <ø> (ø)`
core/device_hooks/dpcpp_hooks.cpp	`34.78% <ø> (ø)`
core/test/utils/unsort_matrix.hpp	`78.37% <ø> (ø)`
include/ginkgo/core/base/abstract_factory.hpp	`87.09% <ø> (ø)`
include/ginkgo/core/base/array.hpp	`94.78% <ø> (ø)`
include/ginkgo/core/base/combination.hpp	`83.33% <ø> (ø)`
include/ginkgo/core/base/composition.hpp	`92.00% <ø> (ø)`
include/ginkgo/core/base/dim.hpp	`88.88% <ø> (ø)`
include/ginkgo/core/base/exception.hpp	`100.00% <ø> (ø)`
... and 63 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 1cbdc8b...562f290. Read the comment docs.

Slaedr · 2020-12-03T09:55:20Z

dev_tools/scripts/config

@@ -6,10 +6,26 @@
 - FixInclude: "hip/hip_runtime.h"


What's the purpose of this file?

You mean hip_runtime? It contains all the macros like hipLaunchKernelGGL, HIP_KERNEL_NAME, device-side assert etc.

No, I meant this entire config file, haha. I guess it's unrelated to this PR but I have no idea what's going on here.

This file configures the format_header.sh script by fixing a few special-cases where the default detection of the main header belonging to a file (the one that is included at the top) doesn't work properly

Slaedr · 2020-12-03T10:05:33Z

.github/workflows/bot-pr-comment.yml

@@ -14,7 +14,7 @@ jobs:
 fetch-depth: 0
 - name: Add appropriate labels
 env:
- GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ GITHUB_TOKEN: ${{ secrets.BOT_TOKEN }}


What's the difference between secrets.GITHUB_TOKEN and secrets.BOT_TOKEN?

GITHUB_TOKEN is an automatically generated and temporary token for github-actions[bot], which has the annoying property that pushes from this token don't trigger subsequent Github Actions (like Windows/macOS CI jobs) to avoid infinite loops in Github Actions by default.
BOT_TOKEN is a manually generated personal authentication token for @ginkgo-bot (stored in this repo's Secrets) which circumvents this limitation.
So in the future, comments will come from ginkgo-bot instead of github-actions[bot] and the CI jobs will run after every push

Slaedr

LGTM. Just a couple of questions.

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

upsj requested review from yhmtsai, thoasm, fritzgoebel, pratikvn, Slaedr and tcojean December 2, 2020 12:29

upsj self-assigned this Dec 2, 2020

upsj added the 1:ST:ready-for-review This PR is ready for review label Dec 2, 2020

upsj removed type:solver This is related to the solvers type:stopping-criteria This is related to the stopping criteria labels Dec 2, 2020

tcojean approved these changes Dec 2, 2020

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upsj added 2 commits December 2, 2020 19:22

format everything

ec35793

update bot to delete old comments

1b280ba

upsj force-pushed the format_all branch from 2d65cc8 to 1b280ba Compare December 2, 2020 18:36

fix ISAI test include

562f290

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upsj merged commit cb331de into develop Dec 3, 2020

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		@@ -44,7 +44,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.


		#include "core/components/prefix_sum.hpp"
		#include "core/factorization/par_ilut_kernels.hpp"

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