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Add new interface for RCM #1418

Merged
merged 9 commits into from
Oct 30, 2023
Merged

Add new interface for RCM #1418

merged 9 commits into from
Oct 30, 2023

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upsj
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@upsj upsj commented Oct 10, 2023 •
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This adds a new Permutation-based interface for the Reverse Cuthill-McKee (RCM) algorithm in line with the AMD and Nested Dissection algorithm. The old interface is deprecated.

Pulled out of #1408

@upsj upsj added the 1:ST:ready-for-review This PR is ready for review label Oct 10, 2023
@upsj upsj requested a review from a team October 10, 2023 09:15
@upsj upsj self-assigned this Oct 10, 2023
@ginkgo-bot ginkgo-bot added reg:testing This is related to testing. mod:core This is related to the core module. mod:cuda This is related to the CUDA module. mod:openmp This is related to the OpenMP module. mod:reference This is related to the reference module. type:reordering This is related to the matrix(LinOp) reordering labels Oct 10, 2023
MarcelKoch
MarcelKoch requested changes Oct 10, 2023
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LGTM. IMO deprecating the old interface and adding a bit of documentation to the new interface is necessary.

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@upsj upsj changed the base branch from develop to scaled_permutation October 13, 2023 06:53
MarcelKoch
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LGTM. I guess rebasing is necessary.

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core/test/reorder/rcm.cpp
@@ -33,6 +33,17 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#include <ginkgo/core/reorder/rcm.hpp>


#if defined(__GNUC__) || defined(__clang__)
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The documentation on these pragmas is not very clear. I'm unsure how leaving out the corresponding pop effects warnings for other files. But, I would guess it doesn't affect those.

pratikvn
pratikvn approved these changes Oct 13, 2023
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Some doc clarifications, but otherwise looks good.

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yhmtsai commented Oct 13, 2023

need pull request description

@tcojean tcojean added this to the Release 1.7.0 milestone Oct 16, 2023
@upsj upsj force-pushed the scaled_permutation branch 2 times, most recently from 5668746 to 67152e9 Compare October 27, 2023 13:44
Base automatically changed from scaled_permutation to develop October 28, 2023 03:02
@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 Oct 28, 2023
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upsj commented Oct 29, 2023

format!

ginkgo-bot and others added 2 commits October 29, 2023 20:15
@upsj upsj merged commit 565ec65 into develop Oct 30, 2023
12 of 15 checks passed
@upsj upsj deleted the new_rcm_interface branch October 30, 2023 02:39
@tcojean tcojean mentioned this pull request Nov 6, 2023
Merged
tcojean added a commit that referenced this pull request Nov 10, 2023
@tcojean
Merge Release 1.7.0 to master
49242ff 
Release 1.7.0 to master

The Ginkgo team is proud to announce the new Ginkgo minor release 1.7.0. This release brings new features such as:
- Complete GPU-resident sparse direct solvers feature set and interfaces,
- Improved Cholesky factorization performance,
- A new MC64 reordering,
- Batched iterative solver support with the BiCGSTAB solver with batched Dense and ELL matrix types,
- MPI support for the SYCL backend,
- Improved ParILU(T)/ParIC(T) preconditioner convergence,
and more!

If you face an issue, please first check our [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues) and the [open issues list](https://github.com/ginkgo-project/ginkgo/issues) and if you do not find a solution, feel free to [open a new issue](https://github.com/ginkgo-project/ginkgo/issues/new/choose) or ask a question using the [github discussions](https://github.com/ginkgo-project/ginkgo/discussions).

Supported systems and requirements:
+ For all platforms, CMake 3.16+
+ C++14 compliant compiler
+ Linux and macOS
  + GCC: 5.5+
  + clang: 3.9+
  + Intel compiler: 2019+
  + Apple Clang: 14.0 is tested. Earlier versions might also work.
  + NVHPC: 22.7+
  + Cray Compiler: 14.0.1+
  + CUDA module: CMake 3.18+, and CUDA 10.1+ or NVHPC 22.7+
  + HIP module: ROCm 4.5+
  + DPC++ module: Intel oneAPI 2022.1+ with oneMKL and oneDPL. Set the CXX compiler to `dpcpp` or `icpx`.
  + MPI: standard version 3.1+, ideally GPU Aware, for best performance
+ Windows
  + MinGW: GCC 5.5+
  + Microsoft Visual Studio: VS 2019+
  + CUDA module: CUDA 10.1+, Microsoft Visual Studio
  + OpenMP module: MinGW.

### Version support changes

+ CUDA 9.2 is no longer supported and 10.0 is untested [#1382](#1382)
+ Ginkgo now requires CMake version 3.16 (and 3.18 for CUDA) [#1368](#1368)

### Interface changes

+ `const` Factory parameters can no longer be modified through `with_*` functions, as this breaks const-correctness [#1336](#1336) [#1439](#1439)

### New Deprecations

+ The `device_reset` parameter of CUDA and HIP executors no longer has an effect, and its `allocation_mode` parameters have been deprecated in favor of the `Allocator` interface. [#1315](#1315)
+ The CMake parameter `GINKGO_BUILD_DPCPP` has been deprecated in favor of `GINKGO_BUILD_SYCL`. [#1350](#1350)
+ The `gko::reorder::Rcm` interface has been deprecated in favor of `gko::experimental::reorder::Rcm` based on `Permutation`. [#1418](#1418)
+ The Permutation class' `permute_mask` functionality. [#1415](#1415)
+ Multiple functions with typos (`set_complex_subpsace()`, range functions such as `conj_operaton` etc). [#1348](#1348)

### Summary of previous deprecations
+ `gko::lend()` is not necessary anymore.
+ The classes `RelativeResidualNorm` and `AbsoluteResidualNorm` are deprecated in favor of `ResidualNorm`.
+ The class `AmgxPgm` is deprecated in favor of `Pgm`.
+ Default constructors for the CSR `load_balance` and `automatical` strategies
+ The PolymorphicObject's move-semantic `copy_from` variant
+ The templated `SolverBase` class.
+ The class `MachineTopology` is deprecated in favor of `machine_topology`.
+ Logger constructors and create functions with the `executor` parameter.
+ The virtual, protected, Dense functions `compute_norm1_impl`, `add_scaled_impl`, etc.
+ Logger events for solvers and criterion without the additional `implicit_tau_sq` parameter.
+ The global `gko::solver::default_krylov_dim`, use instead `gko::solver::gmres_default_krylov_dim`.

### Added features

+ Adds a batch::BatchLinOp class that forms a base class for batched linear operators such as batched matrix formats, solver and preconditioners [#1379](#1379)
+ Adds a batch::MultiVector class that enables operations such as dot, norm, scale on batched vectors [#1371](#1371)
+ Adds a batch::Dense matrix format that stores batched dense matrices and provides gemv operations for these dense matrices. [#1413](#1413)
+ Adds a batch::Ell matrix format that stores batched Ell matrices and provides spmv operations for these batched Ell matrices. [#1416](#1416) [#1437](#1437)
+ Add a batch::Bicgstab solver (class, core, and reference kernels) that enables iterative solution of batched linear systems [#1438](#1438).
+ Add device kernels (CUDA, HIP, and DPCPP) for batch::Bicgstab solver. [#1443](#1443).
+ New MC64 reordering algorithm which optimizes the diagonal product or sum of a matrix by permuting the rows, and computes additional scaling factors for equilibriation [#1120](#1120)
+ New interface for (non-symmetric) permutation and scaled permutation of Dense and Csr matrices [#1415](#1415)
+ LU and Cholesky Factorizations can now be separated into their factors [#1432](#1432)
+ New symbolic LU factorization algorithm that is optimized for matrices with an almost-symmetric sparsity pattern [#1445](#1445)
+ Sorting kernels for SparsityCsr on all backends [#1343](#1343)
+ Allow passing pre-generated local solver as factory parameter for the distributed Schwarz preconditioner [#1426](#1426)
+ Add DPCPP kernels for Partition [#1034](#1034), and CSR's `check_diagonal_entries` and `add_scaled_identity` functionality [#1436](#1436)
+ Adds a helper function to create a partition based on either local sizes, or local ranges [#1227](#1227)
+ Add function to compute arithmetic mean of dense and distributed vectors [#1275](#1275)
+ Adds `icpx` compiler supports [#1350](#1350)
+ All backends can be built simultaneously [#1333](#1333)
+ Emits a CMake warning in downstream projects that use different compilers than the installed Ginkgo [#1372](#1372)
+ Reordering algorithms in sparse_blas benchmark [#1354](#1354)
+ Benchmarks gained an `-allocator` parameter to specify device allocators [#1385](#1385)
+ Benchmarks gained an `-input_matrix` parameter that initializes the input JSON based on the filename [#1387](#1387)
+ Benchmark inputs can now be reordered as a preprocessing step [#1408](#1408)


### Improvements

+ Significantly improve Cholesky factorization performance [#1366](#1366)
+ Improve parallel build performance [#1378](#1378)
+ Allow constrained parallel test execution using CTest resources [#1373](#1373)
+ Use arithmetic type more inside mixed precision ELL [#1414](#1414)
+ Most factory parameters of factory type no longer need to be constructed explicitly via `.on(exec)` [#1336](#1336) [#1439](#1439)
+ Improve ParILU(T)/ParIC(T) convergence by using more appropriate atomic operations [#1434](#1434)

### Fixes

+ Fix an over-allocation for OpenMP reductions [#1369](#1369)
+ Fix DPCPP's common-kernel reduction for empty input sizes [#1362](#1362)
+ Fix several typos in the API and documentation [#1348](#1348)
+ Fix inconsistent `Threads` between generations [#1388](#1388)
+ Fix benchmark median condition [#1398](#1398)
+ Fix HIP 5.6.0 compilation [#1411](#1411)
+ Fix missing destruction of rand_generator from cuda/hip [#1417](#1417)
+ Fix PAPI logger destruction order [#1419](#1419)
+ Fix TAU logger compilation [#1422](#1422)
+ Fix relative criterion to not iterate if the residual is already zero [#1079](#1079)
+ Fix memory_order invocations with C++20 changes [#1402](#1402)
+ Fix `check_diagonal_entries_exist` report correctly when only missing diagonal value in the last rows. [#1440](#1440)
+ Fix checking OpenMPI version in cross-compilation settings [#1446](#1446)
+ Fix false-positive deprecation warnings in Ginkgo, especially for the old Rcm (it doesn't emit deprecation warnings anymore as a result but is still considered deprecated) [#1444](#1444)


### Related PR: #1451
tcojean added a commit that referenced this pull request Nov 10, 2023
@tcojean
Merge Release 1.7.0 to develop
86f5164 
Release 1.7.0 to develop

The Ginkgo team is proud to announce the new Ginkgo minor release 1.7.0. This release brings new features such as:
- Complete GPU-resident sparse direct solvers feature set and interfaces,
- Improved Cholesky factorization performance,
- A new MC64 reordering,
- Batched iterative solver support with the BiCGSTAB solver with batched Dense and ELL matrix types,
- MPI support for the SYCL backend,
- Improved ParILU(T)/ParIC(T) preconditioner convergence,
and more!

If you face an issue, please first check our [known issues page](https://github.com/ginkgo-project/ginkgo/wiki/Known-Issues) and the [open issues list](https://github.com/ginkgo-project/ginkgo/issues) and if you do not find a solution, feel free to [open a new issue](https://github.com/ginkgo-project/ginkgo/issues/new/choose) or ask a question using the [github discussions](https://github.com/ginkgo-project/ginkgo/discussions).

Supported systems and requirements:
+ For all platforms, CMake 3.16+
+ C++14 compliant compiler
+ Linux and macOS
  + GCC: 5.5+
  + clang: 3.9+
  + Intel compiler: 2019+
  + Apple Clang: 14.0 is tested. Earlier versions might also work.
  + NVHPC: 22.7+
  + Cray Compiler: 14.0.1+
  + CUDA module: CMake 3.18+, and CUDA 10.1+ or NVHPC 22.7+
  + HIP module: ROCm 4.5+
  + DPC++ module: Intel oneAPI 2022.1+ with oneMKL and oneDPL. Set the CXX compiler to `dpcpp` or `icpx`.
  + MPI: standard version 3.1+, ideally GPU Aware, for best performance
+ Windows
  + MinGW: GCC 5.5+
  + Microsoft Visual Studio: VS 2019+
  + CUDA module: CUDA 10.1+, Microsoft Visual Studio
  + OpenMP module: MinGW.

### Version support changes

+ CUDA 9.2 is no longer supported and 10.0 is untested [#1382](#1382)
+ Ginkgo now requires CMake version 3.16 (and 3.18 for CUDA) [#1368](#1368)

### Interface changes

+ `const` Factory parameters can no longer be modified through `with_*` functions, as this breaks const-correctness [#1336](#1336) [#1439](#1439)

### New Deprecations

+ The `device_reset` parameter of CUDA and HIP executors no longer has an effect, and its `allocation_mode` parameters have been deprecated in favor of the `Allocator` interface. [#1315](#1315)
+ The CMake parameter `GINKGO_BUILD_DPCPP` has been deprecated in favor of `GINKGO_BUILD_SYCL`. [#1350](#1350)
+ The `gko::reorder::Rcm` interface has been deprecated in favor of `gko::experimental::reorder::Rcm` based on `Permutation`. [#1418](#1418)
+ The Permutation class' `permute_mask` functionality. [#1415](#1415)
+ Multiple functions with typos (`set_complex_subpsace()`, range functions such as `conj_operaton` etc). [#1348](#1348)

### Summary of previous deprecations
+ `gko::lend()` is not necessary anymore.
+ The classes `RelativeResidualNorm` and `AbsoluteResidualNorm` are deprecated in favor of `ResidualNorm`.
+ The class `AmgxPgm` is deprecated in favor of `Pgm`.
+ Default constructors for the CSR `load_balance` and `automatical` strategies
+ The PolymorphicObject's move-semantic `copy_from` variant
+ The templated `SolverBase` class.
+ The class `MachineTopology` is deprecated in favor of `machine_topology`.
+ Logger constructors and create functions with the `executor` parameter.
+ The virtual, protected, Dense functions `compute_norm1_impl`, `add_scaled_impl`, etc.
+ Logger events for solvers and criterion without the additional `implicit_tau_sq` parameter.
+ The global `gko::solver::default_krylov_dim`, use instead `gko::solver::gmres_default_krylov_dim`.

### Added features

+ Adds a batch::BatchLinOp class that forms a base class for batched linear operators such as batched matrix formats, solver and preconditioners [#1379](#1379)
+ Adds a batch::MultiVector class that enables operations such as dot, norm, scale on batched vectors [#1371](#1371)
+ Adds a batch::Dense matrix format that stores batched dense matrices and provides gemv operations for these dense matrices. [#1413](#1413)
+ Adds a batch::Ell matrix format that stores batched Ell matrices and provides spmv operations for these batched Ell matrices. [#1416](#1416) [#1437](#1437)
+ Add a batch::Bicgstab solver (class, core, and reference kernels) that enables iterative solution of batched linear systems [#1438](#1438).
+ Add device kernels (CUDA, HIP, and DPCPP) for batch::Bicgstab solver. [#1443](#1443).
+ New MC64 reordering algorithm which optimizes the diagonal product or sum of a matrix by permuting the rows, and computes additional scaling factors for equilibriation [#1120](#1120)
+ New interface for (non-symmetric) permutation and scaled permutation of Dense and Csr matrices [#1415](#1415)
+ LU and Cholesky Factorizations can now be separated into their factors [#1432](#1432)
+ New symbolic LU factorization algorithm that is optimized for matrices with an almost-symmetric sparsity pattern [#1445](#1445)
+ Sorting kernels for SparsityCsr on all backends [#1343](#1343)
+ Allow passing pre-generated local solver as factory parameter for the distributed Schwarz preconditioner [#1426](#1426)
+ Add DPCPP kernels for Partition [#1034](#1034), and CSR's `check_diagonal_entries` and `add_scaled_identity` functionality [#1436](#1436)
+ Adds a helper function to create a partition based on either local sizes, or local ranges [#1227](#1227)
+ Add function to compute arithmetic mean of dense and distributed vectors [#1275](#1275)
+ Adds `icpx` compiler supports [#1350](#1350)
+ All backends can be built simultaneously [#1333](#1333)
+ Emits a CMake warning in downstream projects that use different compilers than the installed Ginkgo [#1372](#1372)
+ Reordering algorithms in sparse_blas benchmark [#1354](#1354)
+ Benchmarks gained an `-allocator` parameter to specify device allocators [#1385](#1385)
+ Benchmarks gained an `-input_matrix` parameter that initializes the input JSON based on the filename [#1387](#1387)
+ Benchmark inputs can now be reordered as a preprocessing step [#1408](#1408)


### Improvements

+ Significantly improve Cholesky factorization performance [#1366](#1366)
+ Improve parallel build performance [#1378](#1378)
+ Allow constrained parallel test execution using CTest resources [#1373](#1373)
+ Use arithmetic type more inside mixed precision ELL [#1414](#1414)
+ Most factory parameters of factory type no longer need to be constructed explicitly via `.on(exec)` [#1336](#1336) [#1439](#1439)
+ Improve ParILU(T)/ParIC(T) convergence by using more appropriate atomic operations [#1434](#1434)

### Fixes

+ Fix an over-allocation for OpenMP reductions [#1369](#1369)
+ Fix DPCPP's common-kernel reduction for empty input sizes [#1362](#1362)
+ Fix several typos in the API and documentation [#1348](#1348)
+ Fix inconsistent `Threads` between generations [#1388](#1388)
+ Fix benchmark median condition [#1398](#1398)
+ Fix HIP 5.6.0 compilation [#1411](#1411)
+ Fix missing destruction of rand_generator from cuda/hip [#1417](#1417)
+ Fix PAPI logger destruction order [#1419](#1419)
+ Fix TAU logger compilation [#1422](#1422)
+ Fix relative criterion to not iterate if the residual is already zero [#1079](#1079)
+ Fix memory_order invocations with C++20 changes [#1402](#1402)
+ Fix `check_diagonal_entries_exist` report correctly when only missing diagonal value in the last rows. [#1440](#1440)
+ Fix checking OpenMPI version in cross-compilation settings [#1446](#1446)
+ Fix false-positive deprecation warnings in Ginkgo, especially for the old Rcm (it doesn't emit deprecation warnings anymore as a result but is still considered deprecated) [#1444](#1444)

### Related PR: #1454
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@pratikvn pratikvn pratikvn approved these changes

@MarcelKoch MarcelKoch MarcelKoch approved these changes

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