Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Extract prefix sum computations #429

Merged
merged 4 commits into from
Jan 13, 2020
Merged

Extract prefix sum computations #429

merged 4 commits into from
Jan 13, 2020

Conversation

upsj
Copy link
Member

@upsj upsj commented Dec 19, 2019 •
edited
Loading

This PR introduces a new prefix_sum kernel that is used instead of manually computing prefix sums in different places. This also fixes two bugs:

  • In CUDA/HIP ParILU, the wrong num_blocks is used for launching the prefix sum kernels
  • In Reference ParILU, the handling of non-existent diagonals is incorrect.

Finally, it removes a few unnecessary calls to Array::clear since they would be cleaned up via RAII anyways.

@upsj upsj added is:bug Something looks wrong. is:technical-debt This is aimed at reducing technical debt. labels Dec 19, 2019
@upsj upsj requested review from thoasm, yhmtsai and tcojean December 19, 2019 10:01
@upsj upsj self-assigned this Dec 19, 2019
@upsj upsj force-pushed the rowptrs_kernel branch 3 times, most recently from 28c057e to d3ee1ec Compare December 19, 2019 12:15
thoasm
thoasm reviewed Dec 19, 2019
View reviewed changes
Copy link
Member

@thoasm thoasm left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Some comments on the code (mostly that the inclusion of the prefix header can be removed).

cuda/matrix/csr_kernels.cu Outdated Show resolved Hide resolved
cuda/matrix/dense_kernels.cu Outdated Show resolved Hide resolved
cuda/matrix/ell_kernels.cu Outdated Show resolved Hide resolved
cuda/matrix/hybrid_kernels.cu Show resolved Hide resolved
hip/factorization/par_ilu_kernels.hip.cpp Outdated Show resolved Hide resolved
hip/matrix/csr_kernels.hip.cpp Outdated Show resolved Hide resolved
hip/matrix/dense_kernels.hip.cpp Show resolved Hide resolved
reference/factorization/par_ilu_kernels.cpp Outdated Show resolved Hide resolved
@upsj upsj force-pushed the rowptrs_kernel branch 4 times, most recently from 65bbf24 to 52ae4e5 Compare December 22, 2019 16:48
pratikvn
pratikvn approved these changes Jan 6, 2020
View reviewed changes
Copy link
Member

@pratikvn pratikvn left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM!

A question: prefix_sum seems to be more of a general algorithm than being just restricted to matrices. So, is {exec}/matrix/common_kernels.x the right place to put these ?

hip/matrix/dense_kernels.hip.cpp Show resolved Hide resolved
@upsj
Copy link
Member Author

upsj commented Jan 6, 2020

@pratikvn No, you are probably right. So would something like */component/prefix_sum.* make more sense? Also I should at least add 1-2 tests for this kernel.

@upsj upsj added the 1:ST:ready-for-review This PR is ready for review label Jan 8, 2020
@pratikvn
Copy link
Member

pratikvn commented Jan 9, 2020

@upsj , Yes, that sounds good to me.

yhmtsai
yhmtsai reviewed Jan 10, 2020
View reviewed changes
Copy link
Member

@yhmtsai yhmtsai left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should cuda/test/components/prefix_sum.cu be cuda/test/components/prefix_sum.cpp enough?
Others (without par_ilu) look good to me.
Do you want to solve the par_ilu here? or another PR.

@upsj
Copy link
Member Author

upsj commented Jan 10, 2020

Do you want to solve the par_ilu here? or another PR.

No, that would involve having to add another kernel, I will have to do that in another PR.

yhmtsai
yhmtsai approved these changes Jan 12, 2020
View reviewed changes
Copy link
Member

@yhmtsai yhmtsai left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM. some minor format changes

hip/components/prefix_sum.hip.cpp Show resolved Hide resolved
cuda/components/prefix_sum.cu Outdated Show resolved Hide resolved
hip/components/prefix_sum.hip.cpp Show resolved Hide resolved
omp/components/prefix_sum.cpp Show resolved Hide resolved
reference/components/prefix_sum.cpp Show resolved Hide resolved
upsj
upsj commented Jan 12, 2020
View reviewed changes
cuda/components/prefix_sum.cu Outdated Show resolved Hide resolved
upsj
upsj commented Jan 12, 2020
View reviewed changes
omp/components/prefix_sum.cpp Outdated Show resolved Hide resolved
@upsj upsj added 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 Jan 12, 2020
upsj added 2 commits January 12, 2020 21:58
@upsj
extract prefix sum computations
db2ffaf 
* introduce a new `prefix_sum` kernel that is used instead
* remove a few unnecessary `Array::clear` invocations
* fix reference ParILU initialization for zero diagonal entries.
@upsj
move prefix_sum kernel to components
ffbbf8a
upsj and others added 2 commits January 12, 2020 21:58
@upsj
add prefix_sum tests
bfa9a80
@upsj @yhmtsai
improve formatting
4abd1eb 
Co-Authored-By: Yuhsiang M. Tsai <yhmtsai@gmail.com>
@upsj upsj merged commit d53f39b into develop Jan 13, 2020
@upsj upsj deleted the rowptrs_kernel branch January 13, 2020 00:15
@sonarqubecloud
Copy link

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

@tcojean tcojean mentioned this pull request Jun 23, 2020
Merged
tcojean added a commit that referenced this pull request Jul 7, 2020
@tcojean
Merge Release 1.2.0
b4be2be 
The Ginkgo team is proud to announce the new minor release of Ginkgo version
1.2.0. This release brings full HIP support to Ginkgo, new preconditioners
(ParILUT, ISAI), conversion between double and float for all LinOps, and many
more features and fixes.

Supported systems and requirements:
+ For all platforms, cmake 3.9+
+ Linux and MacOS
  + gcc: 5.3+, 6.3+, 7.3+, all versions after 8.1+
  + clang: 3.9+
  + Intel compiler: 2017+
  + Apple LLVM: 8.0+
  + CUDA module: CUDA 9.0+
  + HIP module: ROCm 2.8+
+ Windows
  + MinGW and CygWin: gcc 5.3+, 6.3+, 7.3+, all versions after 8.1+
  + Microsoft Visual Studio: VS 2017 15.7+
  + CUDA module: CUDA 9.0+, Microsoft Visual Studio
  + OpenMP module: MinGW or CygWin.


The current known issues can be found in the [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues).


# Additions
Here are the main additions to the Ginkgo library. Other thematic additions are listed below.
+ Add full HIP support to Ginkgo [#344](#344), [#357](#357), [#384](#384), [#373](#373), [#391](#391), [#396](#396), [#395](#395), [#393](#393), [#404](#404), [#439](#439), [#443](#443), [#567](#567)
+ Add a new ISAI preconditioner [#489](#489), [#502](#502), [#512](#512), [#508](#508), [#520](#520)
+ Add support for ParILUT and ParICT factorization with ILU preconditioners [#400](#400)
+ Add a new BiCG solver [#438](#438)
+ Add a new permutation matrix format [#352](#352), [#469](#469)
+ Add CSR SpGEMM support [#386](#386), [#398](#398), [#418](#418), [#457](#457)
+ Add CSR SpGEAM support [#556](#556)
+ Make all solvers and preconditioners transposable [#535](#535)
+ Add CsrBuilder and CooBuilder for intrusive access to matrix arrays [#437](#437)
+ Add a standard-compliant allocator based on the Executors [#504](#504)
+ Support conversions for all LinOp between double and float [#521](#521)
+ Add a new boolean to the CUDA and HIP executors to control DeviceReset (default off) [#557](#557)
+ Add a relaxation factor to IR to represent Richardson Relaxation [#574](#574)
+ Add two new stopping criteria, for relative (to `norm(b)`) and absolute residual norm [#577](#577)

### Example additions
+ Templatize all examples to simplify changing the precision [#513](#513)
+ Add a new adaptive precision block-Jacobi example [#507](#507)
+ Add a new IR example [#522](#522)
+ Add a new Mixed Precision Iterative Refinement example [#525](#525)
+ Add a new example on iterative trisolves in ILU preconditioning [#526](#526), [#536](#536), [#550](#550)

### Compilation and library changes
+ Auto-detect compilation settings based on environment [#435](#435), [#537](#537)
+ Add SONAME to shared libraries [#524](#524)
+ Add clang-cuda support [#543](#543)

### Other additions
+ Add sorting, searching and merging kernels for GPUs [#403](#403), [#428](#428), [#417](#417), [#455](#455)
+ Add `gko::as` support for smart pointers [#493](#493)
+ Add setters and getters for criterion factories [#527](#527)
+ Add a new method to check whether a solver uses `x` as an initial guess [#531](#531)
+ Add contribution guidelines [#549](#549)

# Fixes
### Algorithms
+ Improve the classical CSR strategy's performance [#401](#401)
+ Improve the CSR automatical strategy [#407](#407), [#559](#559)
+ Memory, speed improvements to the ELL kernel [#411](#411)
+ Multiple improvements and fixes to ParILU [#419](#419), [#427](#427), [#429](#429), [#456](#456), [#544](#544)
+ Fix multiple issues with GMRES [#481](#481), [#523](#523), [#575](#575)
+ Optimize OpenMP matrix conversions [#505](#505)
+ Ensure the linearity of the ILU preconditioner [#506](#506)
+ Fix IR's use of the advanced apply [#522](#522)
+ Fix empty matrices conversions and add tests [#560](#560)

### Other core functionalities
+ Fix complex number support in our math header [#410](#410)
+ Fix CUDA compatibility of the main ginkgo header [#450](#450)
+ Fix isfinite issues [#465](#465)
+ Fix the Array::view memory leak and the array/view copy/move [#485](#485)
+ Fix typos preventing use of some interface functions [#496](#496)
+ Fix the `gko::dim` to abide to the C++ standard [#498](#498)
+ Simplify the executor copy interface [#516](#516)
+ Optimize intermediate storage for Composition [#540](#540)
+ Provide an initial guess for relevant Compositions [#561](#561)
+ Better management of nullptr as criterion [#562](#562)
+ Fix the norm calculations for complex support [#564](#564)

### CUDA and HIP specific
+ Use the return value of the atomic operations in our wrappers [#405](#405)
+ Improve the portability of warp lane masks [#422](#422)
+ Extract thread ID computation into a separate function [#464](#464)
+ Reorder kernel parameters for consistency [#474](#474)
+ Fix the use of `pragma unroll` in HIP [#492](#492)

### Other
+ Fix the Ginkgo CMake installation files [#414](#414), [#553](#553)
+ Fix the Windows compilation [#415](#415)
+ Always use demangled types in error messages [#434](#434), [#486](#486)
+ Add CUDA header dependency to appropriate tests [#452](#452)
+ Fix several sonarqube or compilation warnings [#453](#453), [#463](#463), [#532](#532), [#569](#569)
+ Add shuffle tests [#460](#460)
+ Fix MSVC C2398 error [#490](#490)
+ Fix missing interface tests in test install [#558](#558)

# Tools and ecosystem
### Benchmarks
+ Add better norm support in the benchmarks [#377](#377)
+ Add CUDA 10.1 generic SpMV support in benchmarks [#468](#468), [#473](#473)
+ Add sparse library ILU in benchmarks [#487](#487)
+ Add overhead benchmarking capacities [#501](#501)
+ Allow benchmarking from a matrix list file [#503](#503)
+ Fix benchmarking issue with JSON and non-finite numbers [#514](#514)
+ Fix benchmark logger crashers with OpenMP [#565](#565)

### CI related
+ Improvements to the CI setup with HIP compilation [#421](#421), [#466](#466)
+ Add MacOSX CI support [#470](#470), [#488](#488)
+ Add Windows CI support [#471](#471), [#488](#488), [#510](#510), [#566](#566)
+ Use sanitizers instead of valgrind [#476](#476)
+ Add automatic container generation and update facilities [#499](#499)
+ Fix the CI parallelism settings [#517](#517), [#538](#538), [#539](#539)
+ Make the codecov patch check informational [#519](#519)
+ Add support for LLVM sanitizers with improved thread sanitizer support [#578](#578)

### Test suite
+ Add an assertion for sparsity pattern equality [#416](#416)
+ Add core and reference multiprecision tests support [#448](#448)
+ Speed up GPU tests by avoiding device reset [#467](#467)
+ Change test matrix location string [#494](#494)

### Other
+ Add Ginkgo badges from our tools [#413](#413)
+ Update the `create_new_algorithm.sh` script [#420](#420)
+ Bump copyright and improve license management [#436](#436), [#433](#433)
+ Set clang-format minimum requirement [#441](#441), [#484](#484)
+ Update git-cmake-format [#446](#446), [#484](#484)
+ Disable the development tools by default [#442](#442)
+ Add a script for automatic header formatting [#447](#447)
+ Add GDB pretty printer for `gko::Array` [#509](#509)
+ Improve compilation speed [#533](#533)
+ Add editorconfig support [#546](#546)
+ Add a compile-time check for header self-sufficiency [#552](#552)


# Related PR: #583
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@thoasm thoasm thoasm left review comments

@yhmtsai yhmtsai yhmtsai approved these changes

@pratikvn pratikvn pratikvn approved these changes

@tcojean tcojean Awaiting requested review from tcojean

Assignees

@upsj upsj

Labels
1:ST:ready-to-merge This PR is ready to merge. is:bug Something looks wrong. is:technical-debt This is aimed at reducing technical debt.
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@upsj @pratikvn @thoasm @yhmtsai