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Fix the view memory leak and array/view copy/move. #485

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@tcojean tcojean commented Mar 23, 2020

This fixes some of the discussed issues with arrays. The changes are noted in the list below. Some of these points should still be discussed.

  • Add tests for copy/move of all combinations of array/view.
  • Add a new exception helper macro for testing array dimensions.
  • When copying something into a view, do bound checking and ensure what is
    copied has a compatible amount of data.
  • When copying into an array, the proper amount of data is allocated and copied
    over.
  • When moving a into b, b becomes a and a is invalid afterwards.
  • Resize and reset for views throws an error.

@tcojean tcojean added is:bug Something looks wrong. is:enhancement An improvement of an existing feature. mod:core This is related to the core module. 1:ST:ready-for-review This PR is ready for review labels Mar 23, 2020
@tcojean tcojean self-assigned this Mar 23, 2020
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LGTM, mainly a few suggestions for more restrictive tests.

Concerning your open questions, I agree with most of them, but tend to disagree about the resize_and_reset. In my opinion, it should either turn a view into an array if needed, or set the size to 0 instead of leaving it intact, when the data pointer is a null pointer.

I believe there are two ways we can evaluate the different approaches you presented: By expectations (which behavior would someone intuitively expect) or by convenience (which behavior makes it easiest for us to implement our algorithms, i.e. needs the smallest amount of hacks, workarounds etc.)

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codecov bot commented Mar 24, 2020

Codecov Report

Merging #485 into develop will decrease coverage by 0.05%.
The diff coverage is 100.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #485      +/-   ##
===========================================
- Coverage    88.86%   88.80%   -0.06%     
===========================================
  Files          256      256              
  Lines        16484    16546      +62     
===========================================
+ Hits         14648    14694      +46     
- Misses        1836     1852      +16     
Impacted Files Coverage Δ
include/ginkgo/core/base/exception_helpers.hpp 91.66% <ø> (ø)
core/test/base/array.cpp 100.00% <100.00%> (ø)
include/ginkgo/core/base/array.hpp 96.66% <100.00%> (+0.23%) ⬆️
omp/components/format_conversion.hpp 40.00% <0.00%> (-60.00%) ⬇️
include/ginkgo/core/matrix/ell.hpp 68.75% <0.00%> (-31.25%) ⬇️

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LGTM! Only some minor things.

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Regarding when copying into a view, bounds checking and a throw looks reasonable to me.

The resize_and_reset gets called when moving from an view, right ? In that case, intuitively, to me, setting the pointer to nullptr and not allocating makes sense. I am not sure if it makes sense to decide based on whether something makes implementing our algorithms easier because if the function does something un-intuitive, then using and debugging it becomes a lot harder.

@tcojean tcojean force-pushed the fix_array branch 4 times, most recently from e4c8fe7 to 2cafa07 Compare March 25, 2020 12:40
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Very nice extensive tests, I have some minor comments on them.

I would like to discuss what we intend to do with custom deleter because they could also be a potential problem (can be a potential data leak in the current form).
I am in favor of treating all non-default_deleter as views. That would:

  • (potentially) prevent memory leaks (simply by preventing allocations for non-default_deleters) and
  • make it easier to detect views (and similar)

If we do not allow resizing of views, we might need means to detect if an Array is a view or not (See @upsj example with ILUT or SPGEMM). A public helper function might be useful here.

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I have a question about what's happened if we set_executor on a view?
does it become an array?

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@tcojean tcojean force-pushed the fix_array branch 2 times, most recently from 709406a to c54b520 Compare March 30, 2020 10:26
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LGTM!

@upsj upsj mentioned this pull request Mar 31, 2020
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thoasm commented Apr 1, 2020

@tcojean Can you add a test with a custom deleter and copying of views with mismatching sizes?
That way, we document that this is a potential problem we need to address.

ASSERT_THROW(view1_custom_del = view2, gko::NotSupported);

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tcojean commented Apr 1, 2020

Copying view test with mismatched size is already there I think

ASSERT_THROW(view2 = view_size4, gko::OutOfBoundsError);

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tcojean commented Apr 1, 2020

Anyone has any idea why I get this weird Windows compilation issue? I don't think I changed anything relevant...?

D:\a\ginkgo\ginkgo\core/base/iterator_factory.hpp(297,2): error C2398: Element '2': conversion from 'size_t' to 'gko::detail::IteratorFactory<IndexType,ValueType>::Reference::array_index_type' requires a narrowing conversion [D:\a\ginkgo\ginkgo\build\reference\ginkgo_reference.vcxproj]
          with
          [
              IndexType=gko::int64,
              ValueType=std::complex<double>
          ]
D:\a\ginkgo\ginkgo\core/base/iterator_factory.hpp(296): message : while compiling class template member function 'gko::detail::IteratorFactory<IndexType,ValueType>::Reference gko::detail::IteratorFactory<IndexType,ValueType>::Iterator::operator [](size_t) const' [D:\a\ginkgo\ginkgo\build\reference\ginkgo_reference.vcxproj]
          with
          [
              IndexType=gko::int64,
              ValueType=std::complex<double>
          ]
C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.25.28610\include\algorithm(2749): message : see reference to function template instantiation 'gko::detail::IteratorFactory<IndexType,ValueType>::Reference gko::detail::IteratorFactory<IndexType,ValueType>::Iterator::operator [](size_t) const' being compiled [D:\a\ginkgo\ginkgo\build\reference\ginkgo_reference.vcxproj]
          with
          [
              IndexType=gko::int64,
              ValueType=std::complex<double>
          ]

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upsj commented Apr 1, 2020

#490 simply rebase onto develop

+ Add tests for copy/move of all combinations of array/view.
+ Add a new exception helper macro for testing array dimensions.
+ When copying something into a view, do bound checking and unsure what is
  copied has a compatible amount of data. To discuss.
+ When moving a into b, b becomes a and a is invalid afterwards.
+ Resize and reset for views reset the pointer to nullptr and do not allocate
  anything. To discuss.
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tcojean commented Apr 1, 2020

Thanks... I thought I was already up to date with develop but I guess I missed this one.

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sonarcloud bot commented Apr 1, 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 5 Code Smells

15.4% 15.4% Coverage
0.0% 0.0% Duplication

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LGTM!

@pratikvn pratikvn added the is:affects-performance This is related to something which affects performance. label Apr 2, 2020
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LGTM

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@tcojean tcojean 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 Apr 2, 2020
@tcojean tcojean merged commit a8862f5 into develop Apr 2, 2020
@tcojean tcojean deleted the fix_array branch April 2, 2020 14:55
@tcojean tcojean mentioned this pull request Jun 23, 2020
tcojean added a commit that referenced this pull request Jul 7, 2020
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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