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Add CsrBuilder and CooBuilder for intrusive access to matrix arrays #437

Merged
merged 6 commits into from
Jan 10, 2020
Merged

Add CsrBuilder and CooBuilder for intrusive access to matrix arrays #437

merged 6 commits into from
Jan 10, 2020

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upsj
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@upsj upsj commented Jan 7, 2020 •
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These helper classes allow kernels to resize and otherwise manipulate the variable-sized internal arrays of the Csr and Coo matrix types. Both operations are necessary for the ParILUT implementation.

TODO:

  • use them to simplify the spgemm interface

Closes #385

@upsj upsj added the 1:ST:ready-for-review This PR is ready for review label Jan 7, 2020
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@upsj upsj added 1:ST:WIP This PR is a work in progress. Not ready for review. and removed 1:ST:ready-for-review This PR is ready for review labels Jan 7, 2020
@upsj upsj added 1:ST:ready-for-review This PR is ready for review and removed 1:ST:WIP This PR is a work in progress. Not ready for review. labels Jan 8, 2020
tcojean
tcojean approved these changes Jan 8, 2020
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LGTM. Some minor comments.

core/matrix/coo_builder.hpp Outdated Show resolved Hide resolved
core/test/matrix/csr_builder.cpp Show resolved Hide resolved
pratikvn
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LGTM!

core/matrix/coo_builder.hpp Outdated Show resolved Hide resolved
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yhmtsai commented Jan 9, 2020

Is there any consideration about adding these function into new class CooBuilder not original class Coo?

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upsj commented Jan 9, 2020

The main argument is that we don't want to expose any Array to our users. Instead, we have these helpers that should only be used directly by kernels (which is also why I placed them in core and not include/ginkgo/core)

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yhmtsai commented Jan 9, 2020

It makes sense. Thanks

yhmtsai
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LGTM

@upsj upsj added 1:ST:ready-to-merge This PR is ready to merge. mod:core This is related to the core module. and removed 1:ST:ready-for-review This PR is ready for review labels Jan 9, 2020
upsj and others added 6 commits January 9, 2020 21:00
@upsj
add csr_builder and coo_builder
164403e 
they allow for non-const access to arrays for resizing etc.
@upsj
use matrix builders in spgemm
418982e
@upsj
update srow on csr_builder destruction
3cbf27e 
this also makes both builders non-movable
@upsj
make matrix builder constructors explicit
b21111b
@upsj @tcojean
review updates
05c1ae3 
Co-authored-by: Terry Cojean <terry.cojean@kit.edu>
@upsj
make formatting consistent
8664acf
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sonarcloud bot commented Jan 9, 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 1 Code Smell

13.8% 13.8% Coverage
5.8% 5.8% Duplication

@upsj upsj merged commit 962ad36 into develop Jan 10, 2020
@upsj upsj deleted the matrix_builder branch January 10, 2020 03:32
@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
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@tcojean tcojean tcojean approved these changes

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@thoasm thoasm Awaiting requested review from thoasm

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Intrusive access to matrix formats
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@upsj @yhmtsai @pratikvn @tcojean