Improve crs/bsr sorting performance #2293
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- All interfaces taking raw rowmap/entries views updated to have ncols as another arg (with a default, so backwards compatible) - Wrote bulk sort/permutation based sorting for CRS graph, matrix, and BSR matrix (bulk = one large sort of all the entries, using row-major dense index as keys) - This is more performant for imbalanced entries per row - If matrix dimensions are too large to do bulk sort, fall back to sorting within each row with a thread. Signed-off-by: Brian Kelley <[email protected]>
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Instead of just commenting out the cmake. -DKokkosKernels_ENABLE_SORT_CRS_PERFTEST=ON will enable it (off by default)
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Looks like there is a segfault in the |
Lambda segfaults with nvcc+openmp
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lucbv
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I don't want to leave a massive wall of text in the git log, so here's the full version before I squash it down to a shorter version: |
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The changes exactly match github.com/kokkos/kokkos-kernels/pull/2293. Improves performance of sort_crs_matrix by up to 6.3x.
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* CRS sorting improvements - Wrote bulk sort/permutation based sorting for CRS graph, matrix, and BSR matrix (bulk = one large sort of all the entries, using row-major dense index as keys) - This is more performant for imbalanced entries per row - If matrix dimensions are too large to do bulk sort, fall back to sorting within each row with a thread. * Add perf test for sort_crs_matrix * sort_crs: improve parallel labels * Work around kokkos issue 7036 * sort_crs: replace radix sort lambda with functor (Lambda segfaults with nvcc+openmp) --------- Signed-off-by: Brian Kelley <[email protected]>
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* Restore size_t as default offset, in Tribits builds (#2313) If building KokkosKernels standalone, leave int as the default offset (this was the case since #2140). But if building KokkosKernels as a Trilinos/Tribits package, then make size_t the default offset because this is what the Tpetra stack currently uses. Signed-off-by: Brian Kelley <[email protected]> * Improve crs/bsr sorting performance (#2293) * CRS sorting improvements - Wrote bulk sort/permutation based sorting for CRS graph, matrix, and BSR matrix (bulk = one large sort of all the entries, using row-major dense index as keys) - This is more performant for imbalanced entries per row - If matrix dimensions are too large to do bulk sort, fall back to sorting within each row with a thread. * Add perf test for sort_crs_matrix * sort_crs: improve parallel labels * Work around kokkos issue 7036 * sort_crs: replace radix sort lambda with functor (Lambda segfaults with nvcc+openmp) --------- Signed-off-by: Brian Kelley <[email protected]> * SpAdd handle: delete sort_option getter/setter (#2296) SpAdd handle was originally a copy-paste of the spgemm handle way back in #122, and included get_sort_option() and set_sort_option() from spgemm. But these try to use the member bool sort_option, which doesn't exist. Somehow these functions never produced compile errors until someone tried to call them. * Improve GH action to produce release artifacts (#2312) * coo2csr: add parens to function calls (#2318) * Update changelog * Update master_history.txt * .github/workflows: Group jobs under common github-AT2 name (#2320) * Update master_history.txt --------- Signed-off-by: Brian Kelley <[email protected]> Co-authored-by: brian-kelley <[email protected]> Co-authored-by: Damien L-G <[email protected]> Co-authored-by: Carl Pearson <[email protected]> Co-authored-by: Evan Harvey <[email protected]>
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Sep 13, 2024
* Set version number to 4.4.01 * [4.4.01] Patches to 4.4.01 (#2327) * Restore size_t as default offset, in Tribits builds (#2313) If building KokkosKernels standalone, leave int as the default offset (this was the case since #2140). But if building KokkosKernels as a Trilinos/Tribits package, then make size_t the default offset because this is what the Tpetra stack currently uses. Signed-off-by: Brian Kelley <[email protected]> * Improve crs/bsr sorting performance (#2293) * CRS sorting improvements - Wrote bulk sort/permutation based sorting for CRS graph, matrix, and BSR matrix (bulk = one large sort of all the entries, using row-major dense index as keys) - This is more performant for imbalanced entries per row - If matrix dimensions are too large to do bulk sort, fall back to sorting within each row with a thread. * Add perf test for sort_crs_matrix * sort_crs: improve parallel labels * Work around kokkos issue 7036 * sort_crs: replace radix sort lambda with functor (Lambda segfaults with nvcc+openmp) --------- Signed-off-by: Brian Kelley <[email protected]> * SpAdd handle: delete sort_option getter/setter (#2296) SpAdd handle was originally a copy-paste of the spgemm handle way back in #122, and included get_sort_option() and set_sort_option() from spgemm. But these try to use the member bool sort_option, which doesn't exist. Somehow these functions never produced compile errors until someone tried to call them. * Improve GH action to produce release artifacts (#2312) * coo2csr: add parens to function calls (#2318) * Update changelog * Update master_history.txt * .github/workflows: Group jobs under common github-AT2 name (#2320) * Update master_history.txt --------- Signed-off-by: Brian Kelley <[email protected]> Co-authored-by: brian-kelley <[email protected]> Co-authored-by: Damien L-G <[email protected]> Co-authored-by: Carl Pearson <[email protected]> Co-authored-by: Evan Harvey <[email protected]> * Update master_history.txt for 4.4.01 --------- Signed-off-by: Brian Kelley <[email protected]> Co-authored-by: brian-kelley <[email protected]> Co-authored-by: Damien L-G <[email protected]> Co-authored-by: Carl Pearson <[email protected]> Co-authored-by: Evan Harvey <[email protected]>
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Nov 25, 2024
* Fix2130 (#2132) * Fix #2130 - Do not call BsrMatrix spmv impl if block size is 1 - Instead, convert it to unmanaged CrsMatrix and call spmv again - cuSPARSE returned an error code in this case - Better performance * Formatting * Remove redundant remove_pointer_t Handle is already a non-pointer type * Benchmark: modifying spmv benchmark to run range of spmv tests (#2135) This could be further automated to run on matrix from suite sparse * Kokkos Kernels: update version guards to drop old version of Kokkos (#2133) Since we are now in the 4.2 series we only support up to 4.1.00. Older version of Kokkos Core will require older version of Kokkos Kernels for compatibility. Once 4.3.00 is out we will move to drop support for the 4.1 series and only keep 4.2 and 4.3 series. * ODE: BDF methods (#1930) * ODE: adding BDF algorithms Implementing BDF formula for stiff ODEs. Orders 1 to 5 are available and tested. The integrators can be called on GPU to solve multiple systems in parallel. * ODE: fixing storage handling for start-up RK stack * ODE: clang-format * ODE: first adaptive version of BDF The current implementation only allows for adaptivity in time, at this point the BDF Step actually converges as expected with first order integration! * ODE: fixing issues with adaptive BDF The unit-test BDF_adaptive now shows the integration of the logistic equation using adaptive time steps and increasing integration order from 1 to 5. * ODE: running BDF on StiffChemistry problem The problem runs fine and is solved but there are oscillations while the behavior of the solution is smooth. More investigation is needed... * BDF: fixing types and template parameters in batched calls Bascially we need template parameters to be more versatile and cannot assume that all rank1 views will have the exact same underlying type, for instance layouts can be different. * More fixes for GPUs only in tests this time. * ODE: BDF adaptive, fix small bug After adding rhs and update vectors to temp the subviews taken for other variables need to be offset appropriately... * Revert "More fixes for GPUs only in tests this time." This reverts commit 2f70432761485bc6a4c65a1833e7299dd2c340e2. * Revert "Revert "More fixes for GPUs only in tests this time."" This reverts commit 836012bb529551727b3f5913057acad94dfe60df. * ODE: BDF small change to temporarily avoid compile time issue True fix involving a KOKKOS_VERSION check is upcoming after more tests on GPU side... * ODE: BDF fix for some printf statements that will go away soon... * ODE: adding benchmark for BDF The benchmark helps us monitor the performance of the BDF implementaiton across multiple platforms as well as impact of changes over time. * ODE: improve benchmark interface... * ODE: BDF changes to use RMS norm and change some default values Small changes to compare more closely with reference implementation. Some of these might be reverted eventually but that's fine for now. * ODE: BDF convergence more stable and results look pretty good now! Changing the Newton solver convergence criteria as well as changing a few default input parameters leads to a more stable algorithms which can now integrate the stiff Henderson autocatalytic example well in 66 time steps instead of 200k for fixed order integration... * ODE: BDF fix bug in initial time step calculation The initial step routine was overwriting the initial right hand side which led to obvious issues further down the road... now things should work fine. Need to figure out if I can re-initialize the variables in the perf test while excluding that time from each iteration. * ODE: BDF removing bad print statement... std::cout in device code * ODE - BDF: improving perf test Basically adding new untimed setup within the main loop of the benchmark to reset the intial conditions, buffers and vectors ahead of each iteration. * Modifying unit-test to catch proper return type * Applying clang-format * cm_test_all_sandia: update caraway compilers add rocm/5.6.1 and rocm/6.0.0, and openblas/0.3.23 as tpl * Sparse MKL: changing the location of the MKL_SAFE_CALL macro (#2134) * Sparse MKL: changing the location of the MKL_SAFE_CALL macro Moving the macro outside of namespaces to ensure that it will be interpreted correctly when called from any other location in the library. It does not make much sense to guard Impl code in the Experimental namespace and in this case it cleans up a problem with namespace disambiguation for the compiler... * Sparse BsrSpMV: removing Experimental namespace from Impl namespace * Applying clang-format * Sparse SpMV: fixing more namespace issues! * Fixing missing descriptor for bsr spmv * Kokkos Kernels: change the default offset ETI from size_t to int (#2140) This change makes it easier for customer to leverage TPL support which almost always requires offset=int, ordinal=int to be enabled meaning that no TPL support is available with our default ETI... * KokkosSparse_spmv_bsrmatrix_spec: fix Bsr_TC_Precision namespacing Resolve compilation errors in nightly cuda/12.2 A100 build * Drop comment for cleaner clang-format fix * Fix usage of RAII to set cusparse/rocsparse stream (#2141) Temporary objects like "A()" get destructed immediately. For the object to have scope lifetime, it needs a name like "A a();". This was causing cusparse/rocsparse spmv to always execute on the default stream, causing incorrect timing in the spmv perf test. * Use execution space operator== (#2136) It actually is part of the public interface * cm_test_all_sandia: more caraway module updates and cleanup (#2145) * Spmv perftest improvements (#2146) * Spmv perf test improvements - Add option to flush caches by filling a dummy buffer between iterations - Add option to call the non-reuse interface instead of handle/reuse interface - Fix modes T, H in nonsquare case (make x,y the correct length) * Fix mode help text * KokkosKernels Utils: cleaning the zero_vector interface One of the overload requires an unused template, removing that extraneous template and simplify how that function is called in a second overload. * Kokkos Kernels: fixing call to zero_vector in Gauss-Seidel * CMakeLists.txt: Update develop to 4.3.99 * Address reviewer comments * Update CMakeLists.txt Co-authored-by: brian-kelley <[email protected]> * cm_test_all_sandia: solo updates module updates post TOSS upgrade * Fix signed/unsigned comparison warnings (#2150) This is only hit when spmv is called with integer scalars, which doesn't happen in our CI but does often in Tpetra. * SPMV tpl fixes, cusparse workaround (#2152) * SPMV tpl fixes, workaround * Avoid possible integer conversion warnings * Document cusparseSpMM algos that were tested * Applying clang-format * Use default_size_type as default offset in matrix types (#2149) Now a declaration like CrsMatrix<Scalar, Ordinal, Device> will by default use an ETI'd type combination (as int is the default ETI'd offset) * spmv bsr perftest: move fences to right place (#2153) * Kokkos Kernels: removing old code branches ahead of 4.3.00 release (#2139) Some old code branches kept for compatibility with Kokkos Core versions less than 4.2.00 are dropped after release 4.3.00. The largest changes are the removal of support the Kokkos print macro in favor of Kokkos::printf() and the removal of half support from Kokkos Kernels since it is now in Kokkos Core. * Code for running performance measurements on ger() (#2082) * Correct flop count * Addressing feedbacks from Luc * Using 'zero()' instead of '0.' * KokkosBlas1_axpby.hpp: change debug macro guard for printInformation (#2157) * KokkosBlas1_axpby.hpp: change debug macro guard for printInformation - resolves test failures in Trilinos (MueLu) that rely on gold file diff comparisons by removing extra output in debug builds * fix compilation error * Add user tolerance to Serial SVD (#2120) * Add user tolerance to Serial SVD --------- Co-authored-by: whorne <[email protected]> Co-authored-by: Carl Pearson <[email protected]> * Add a simple Harwell-Boeing file reader (#2155) * Add a simple Harwell-Boeing file reader And a test that validates against the MM reader. * Support for symmetrize * This loop can be simplified, there's no diag duplication * Improve IO test * spmv tpls: use correct bool for eti template param (#2160) (It should just be the default, KokkosSpars::Impl::eti_spec_avail<..>::value) * Fix sparse_ioutils test on kokkos-dev (#2162) Adding a ss.sync call fixes it but I have no idea why it was needed here. All the other stringstream reads work fine. * Fix #2156 (#2164) spmv: add special path for rank-2 x/y, but where both have 1 column and a TPL is available for rank-1 but not rank-2. Also call "subhandle->set_exec_space" correctly in the TPLs to ensure proper synchronization between setup, spmv and cleanup (in the case that different exec instances are used in different calls) * Updates from feedback runnig Trilinos testing - Update debug level to > 1 guarding `printInformation(...)` in KokkosBlas1_axpby.hpp to reduce noisy test output - Loosen tolerance of lapack.svd test to avoid random failures that occur near prior tolerance level * Fix #2167: classic MKL doesn't use space instance (#2168) * CHANGELOG.md: 4.3.00 update * KokkosLapack_svd_tpl_spec_decl: defer to MKL spec when LAPACK also enabled Resolves redefintion of struct SVD compilation errors with both MKL and LAPACK are enabled Reported by @maartenarnst in https://github.com/trilinos/Trilinos/issues/12891 Co-authored-by: brian-kelley <[email protected]> * .github/workflows: Added bdw.yml * .github/workflows: Added spr.yml * .github/workflows: Added mi210.yml * .github/workflows: Added h100.yml * .github/workflows: Added volta70.yml * .github/workflows: Added power9.yml and power9_tpls.yml * Jgfouca/block spiluk fixes (#2172) * Progress * Attempt 1, fix multiplication order * Converges in 1 step * Various cleanups * Be sure not to reduce performance of unblocked impl Also add some comments. * Remove test mangling * Fixes for GPU * Fix warning * formatting * Increase eps for floats * This is no longer needed * .github/workflows: Add PR_VEGA908_ROCM561_HIP_SERIAL_LEFT_OPENBLAS_OPENLAPACK_REL * Add guard for cusparse spmv_mv_tpl_spec_avail Address issue #2175 Configuring with magma tpl enabled and cusparse disabled mistakenly triggers the cusparse tpl avail check to be true Guard the KOKKOSSPARSE_SPMV_MV_TPL_SPEC_AVAIL_CUSPARSE macros when CUSPARSE is enabled to prevent this * .github/workflows: Remove OPENLAPACK from names * .github/workflows: Remove power9 until we have hardware to test it on * .github/workflows: Enable rocblas in rocm tpl check * .github/workflows: Remove volta70 until we have hardware to test it on * Add early return if numRows == 0 in trsv to avoid integer divide-by-zero error * Resolves multiple definition of Magma and Cuda singletons (#2178) Address issue #2175 * magma: fix linker errors for builds without cusolver (#2181) * magma: fix linker errors for builds without cusolver * BatchedGemm test: workaround testing cublas+magma - temporary workaround to skip magma test when cublas enabled to avoid issues like #2177 * .github/workflows/mi210: Fix include paths * workflows/osx.yml: test against most recent kokkos tag - test against most recent kokkos release rather than develop branch, as done with AT CI, to avoid compatibility breakages * Resolve vortex compilation issue by resolving (potentially) duplicate symbol (#2183) Stick to pattern of removing leading 'c' or 'z' in method name and relying on the template type Co-authored-by: malphil <[email protected]> * Changes to enable OneAPI usage with Trilinos build (#2185) - Get rid of SYCL_OVERRIDE setting - Add MKL_PROVIDES_BLAS_LAPACK cmake variable and define so that code knows whether to use int, or MKL_INT - Trilinos builds might link with OneAPI for GPU but standard BLAS/LAPACK on CPU * Fix macOS docs build (#2190) * Fix docs build * try docs fix * make sphinx available at config time * GH-Actions: adding security actions and scorecard (#2192) Pretty much taking the new files from PR #2191 and re-creating it in a clean PR on top of develop with small changes relevant to our repository. Cleaning up some workflows to tailor it for our needs * Scorecard: adding manual dispatch and target default branch (#2195) * BsrMatrix: Fix HostMirror typedef (#2196) It needed to have size_type. * update changelog for 4.3.1 * Update CHANGELOG.md * docs.yml: change kokkos version to latest release - avoid version range check issues for release tests * Sparse - SpGEMM: labeling spgemm_symbolic in TPL layer a bit more clearly (#2193) This just improves the readability of the output from the tools as it now has a symbolic matching the numeric phase. Previously we only had spgemm in the label which is a bit confusing as it could be the whole spgemm time i.e. both symbolic and numeric, additionally we had symbolic in the MKL path but not in cusparse, rocsparse... * SpMV: Test NaN, fix NaN handling when beta=0 (#2188) * Test_Sparse_spmv_bsr.hpp: add NaNs to tests * handle NaN in spmv_beta_transpose when beta=0 * handle nan in SpmvMergeHierarchical when beta=0 * Test NaNs in Y, don't reuse modifed Y, catch NaNs in results test * remove unused <iostream> include * explicit casting of zero * Test_sparse_spmv.hpp: remove unused nans parameter * KokkosSparse_spmv.hpp: CUDA11 can't detect this function always returns * Test_Sparse_spmv.hpp: remove unused variable * Run unit tests in correct execution space * Test_Sparse_spmv.hpp: remove unused type aliases * Kokkos::nan() -> KokkosKernels::Impl::quiet_NaN() * Disable cuBLAS dot wrapper (#2206) (not deleted, just guarded with #if 0 and comments explaining) It performs significantly worse than our native impl on 11.2, 11.8 and 12.0 on V100. This is in the dot perf test with a warm-up call. https://github.com/trilinos/Trilinos/issues/12982 was a symptom of this. * Fix spmv regressions (#2204) * Restore cusparse spmv ALG2 path for imbalanced With correct version cutoffs * spmv: use separate rank-1 and rank-2 tpl subhandles * Remove redundant single-column path in native spmv_mv * Fix unused param warning * c++17: add [[fallthrough]] attribute (#1493) * c++17: add [[fallthrough]] attribute * cm_test_all_sandia: -Wimplicit-fallthrough * Enable 3 at2 builds (#2210) * .github/mi210: Enable on PRs * .github/mi210: Disable non-tpl build * .github/bdw: Enable PR_BDW_GNU1020_OPENMP_SERIAL_LEFT_OPENBLAS_REL * .github/h100: Enable PR_HOPPER90_CUDA1180_CUDA_LEFT_RIGHT_REL * Bump ossf/scorecard-action from 2.0.6 to 2.3.3 (#2214) Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.0.6 to 2.3.3. - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](https://github.com/ossf/scorecard-action/compare/99c53751e09b9529366343771cc321ec74e9bd3d...dc50aa9510b46c811795eb24b2f1ba02a914e534) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/upload-artifact from 3.1.3 to 4.3.3 (#2215) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.3 to 4.3.3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/a8a3f3ad30e3422c9c7b888a15615d19a852ae32...65462800fd760344b1a7b4382951275a0abb4808) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/dependency-review-action from 2.5.1 to 4.3.2 (#2217) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 2.5.1 to 4.3.2. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/0efb1d1d84fc9633afcdaad14c485cbbc90ef46c...0c155c5e8556a497adf53f2c18edabf945ed8e70) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump step-security/harden-runner from 2.7.1 to 2.8.0 (#2218) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.7.1 to 2.8.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/a4aa98b93cab29d9b1101a6143fb8bce00e2eac4...f086349bfa2bd1361f7909c78558e816508cdc10) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 2.25.3 to 3.25.6 (#2216) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2.25.3 to 3.25.6. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/ceaec5c11a131e0d282ff3b6f095917d234caace...9fdb3e49720b44c48891d036bb502feb25684276) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Kokkos Kernels: initial security policy (#2220) We state were patches will be made and how to report security vulnerabilities to the project. * Kokkos Kernels: adding SHA for github actions (#2221) * Kokkos Kernels: adding SHA for github actions * Adding sha for docker images * More dependencies fix (#2222) * workflows: fix sha for label checker docker image * workflows: fixing Docker files dependencies. * Fix Docker files (#2223) * SPMV TPLs: improve profile region labels (#2219) - Mark rank-2 versions as "spmv_mv" not "spmv" (the native impl has this, and it's useful to know which one is being run) - Add missing commas separating "BSRMATRIX" and the scalar type name * cusparse spgemm: provide non-null row-ptr (#2213) * Bump github/codeql-action from 3.25.6 to 3.25.7 (#2225) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.6 to 3.25.7. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/9fdb3e49720b44c48891d036bb502feb25684276...f079b8493333aace61c81488f8bd40919487bd9f) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3.6.0 to 4.1.6 (#2226) Bumps [actions/checkout](https://github.com/actions/checkout) from 3.6.0 to 4.1.6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/f43a0e5ff2bd294095638e18286ca9a3d1956744...a5ac7e51b41094c92402da3b24376905380afc29) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * README: adding link to scorecard (#2230) * spmv_mv wrappers for rocsparse (#2233) * spmv_mv wrappers for rocsparse (rocsparse_spmm()) * Use consistent types for alpha/beta in spmv wrappers * Bump step-security/harden-runner from 2.8.0 to 2.8.1 (#2236) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.8.0 to 2.8.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/f086349bfa2bd1361f7909c78558e816508cdc10...17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.25.7 to 3.25.8 (#2237) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.7 to 3.25.8. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/f079b8493333aace61c81488f8bd40919487bd9f...2e230e8fe0ad3a14a340ad0815ddb96d599d2aff) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/dependency-review-action from 4.3.2 to 4.3.3 (#2235) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.3.2 to 4.3.3. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/0c155c5e8556a497adf53f2c18edabf945ed8e70...72eb03d02c7872a771aacd928f3123ac62ad6d3a) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add testing for transpose corner cases (#2234) * Add testing for transpose corner cases crs, bsr, graph: test cases that are 0x0, 100x0 and 0x100. In these cases make sure the matrix generator doesn't try to insert any entries (nnz = 0). * Update sparse/unit_test/Test_Sparse_Transpose.hpp Co-authored-by: Luc Berger <[email protected]> * Update sparse/unit_test/Test_Sparse_Transpose.hpp Co-authored-by: Luc Berger <[email protected]> --------- Co-authored-by: Luc Berger <[email protected]> * Graph: removing executable from repo (#2239) * Fix logic around merge path with TPLs (#2240) SPMV_MERGE_PATH is not always a native algorithm. Add SPMV_NATIVE_MERGE_PATH to cover that case specifically. Test this new option. * spgemm unit test: change matrix value distribution (#2241) Change the distribution A, B values are sampled from so that values in C can't end up close to 0 (as the result of summing terms that are larger). The relative error metric in is_same_matrix is sensitive to this. Fixes #2232 * kokkoskernels_tpls.cmake: remove duplicates arguments when creating argument for exported INTERFACE_INCLUDE_DIRECTORIES Attempt to workaround issue #2238 * Sparse - BsrMatrix: adding new wiki example for documentation (#2228) There is already an example for this but it uses a CrsMatrix as starting point to build a BsrMatrix which is not really helpful in general as the hope is that you can use the BsrMatrix without needing the CrsMatrix as it would double the storage needed... Addressing Kim's comments * Sparse - CrsToBsr: fix type mismatch (#2242) * Update rocsparse algo defaults (#2245) * Update default spmv algorithms for rocsparse - Use stream for common cases (default, fast setup) as it has nearly zero setup cost and performs well for somewhat balanced matrices - Use adaptive (which is rocsparse's default) only if SPMV_MERGE_PATH is the algorithm, as it has a very high setup cost * Re-enable rocsparse spmv for SPMV_FAST_SETUP * In deprecated spmv, fix Controls algorithm mapping (#2246) native -> SPMV_NATIVE native-merge -> SPMV_NATIVE_MERGE_PATH merge -> SPMV_MERGE_PATH tpl -> SPMV_FAST_SETUP * Add batched serial tbsv (#2202) * Add batched serial tbsv * remove incx argument and use strided views instead * Add a new line at the end of files * fix random number generation for complex numbers * remove unused variables from internal tbsv serial functions * remove allclose for testing --------- Co-authored-by: Yuuichi Asahi <[email protected]> * Bump actions/checkout from 4.1.6 to 4.1.7 (#2248) Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.6 to 4.1.7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/a5ac7e51b41094c92402da3b24376905380afc29...692973e3d937129bcbf40652eb9f2f61becf3332) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.25.8 to 3.25.10 (#2249) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.8 to 3.25.10. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/2e230e8fe0ad3a14a340ad0815ddb96d599d2aff...23acc5c183826b7a8a97bce3cecc52db901f8251) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * FindTPLROC*: updates to fix export of import targets Changes for the Rocm tpls to match the handling as done with the Cuda tpls Should resolve issue #2238 * Fix warning about memcpy (#2252) When building Stokhos BlockCrs, this util function gave a warning about memcpy modifying a non-trivially-copyable type. Silence it by casting to void* * RCM fixes, improvements (#2254) * Fix RCM starting vertex issue, improve testing * apply reversing as labels are computed instead of at the end. Saves a loop over all the labels * use min-degree starting vertex within each connected component * spgemm: add profiling regions to native implementations (#2253) * spgemm: add profiling regions to native implementations * Add profiling region to KokkosSPGEMM::KokkosSPGEMM_symbolic * sparse: replace macros with constexpr bools (#2260) * Rename `Impl::alignPtr` to `Impl::alignPtrTo`, allow it to infer argument type (#2261) * KokkosKernels::Impl::alignPtr infers argument type * Rename KokkosKernels::Impl::alignPtr -> alignPtrTo * Bump github/codeql-action from 3.25.10 to 3.25.11 (#2263) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.10 to 3.25.11. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/23acc5c183826b7a8a97bce3cecc52db901f8251...b611370bb5703a7efb587f9d136a52ea24c5c38c) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * sparse: spadd_symbolic fences before device values used on host (#2259) * sparse: spadd_symbolic fences before device values used on host * sparse: use prefix sum to remove explicit spadd fence * sycl: use alternative `alignPtrTo` when SYCL is enabled (SpGEMM) (#2262) * sycl: use alternative alignPtr when SYCL is enabled The current alignPtr, as well as two other alternatives below, do not work on SYCL on Intel PVC. unsigned int f1(unsigned int i, unsigned int align) { return ((i + align - 1) / align * align); } unsigned int f2(unsigned int i, unsigned int align) { return (i + align - 1) & (-align); } * alignPtrTo unit tests * Help gcc/8.3 with ctad issue Resolves #2264 Co-authored-by: Carl Pearson <[email protected]> * Bump actions/upload-artifact from 4.3.3 to 4.3.4 (#2266) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.3.3 to 4.3.4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/65462800fd760344b1a7b4382951275a0abb4808...0b2256b8c012f0828dc542b3febcab082c67f72b) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * handle_t* -> unique_ptr<handle_t> in Bsr SpMV unit tests (#2269) * Workarounds for removed cusparse functions (#2270) cusparse 12.5 removed some functions that were deprecated, like the ILU factorizations and the legacy csrsv (sparse triangular solve) functions. As a workaround, if the cusparse version is >= 12.5 then disable the paths in perftests that call those. * BLAS - gemv: using fallback when mode is 't' or 'c' and onemkl is used (#2272) * Implement batched serial pttrf (#2256) * Batched serial pttrf implementation * fix: use GEMM to add matrices * fix: initialization order * fformat * fix: temporary variable in a test code * fix: docstring of pttrf * check_positive_definitiveness only if KOKKOSKERNELS_DEBUG_LEVEL > 0 * Improve the test for pttrf * fix: int type * fix: cleanup tests for SerialPttrf * cleanup: remove unused deep_copies * fix: docstrings and comments for pttrf * ConjTranspose with conj and Transpose * quick return in pttrf for size 1 or 0 matrix * Add tests for invalid input * fix: info computation --------- Co-authored-by: Yuuichi Asahi <[email protected]> * A little sptrsv cleanup before the main block effort (#2247) * Some cleanup and refactoring * First round of cleanup complete * Fix a couple warnings * formatting * Sparse - SpMV: removing calls to unsuported oneapi - MKL functions (#2274) * Sycl gemv beta (#2276) * BLAS - GEMV: zero out Y when beta == 0 in SYCL TPL code path * BLAS - GEMV: reverting wrong change from previous PR, my bad. * Applying clang-format * Unify alignPtrTo implementation (#2275) * init (#2273) * Bigger sptrsv cleanup (#2280) * Some cleanup and refactoring * Remove Upper/Lower TriLvlSchedTP2SolverFunctors * Remove Upper/Lower single block functors * Remove unused TriLvlSchedTP1SingleBlockFunctorDiagValues and merge upper/lower tri_solve_cg * Merge two big upper/lower branch of tri_solve_chain * Merge upper/lower tri_solve_streams * Switch over block spiluk precond test to use new block sptrsv * Bump actions/dependency-review-action from 4.3.3 to 4.3.4 (#2279) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.3.3 to 4.3.4. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/72eb03d02c7872a771aacd928f3123ac62ad6d3a...5a2ce3f5b92ee19cbb1541a4984c76d921601d7c) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.25.11 to 3.25.12 (#2278) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.11 to 3.25.12. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/b611370bb5703a7efb587f9d136a52ea24c5c38c...4fa2a7953630fd2f3fb380f21be14ede0169dd4f) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Propose increasing column limit to 120. (#2255) * Change key files * Full reformat * Update format.yml * Update ubuntu version for format checker * A couple platforms do not correctly handle static complexes * .github/workflows: Auto trigger AT2 ci upon review (#2243) * Bump github/codeql-action from 3.25.12 to 3.25.13 (#2284) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.12 to 3.25.13. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/4fa2a7953630fd2f3fb380f21be14ede0169dd4f...2d790406f505036ef40ecba973cc774a50395aac) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump step-security/harden-runner from 2.8.1 to 2.9.0 (#2283) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.8.1 to 2.9.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/17d0e2bd7d51742c71671bd19fa12bdc9d40a3d6...0d381219ddf674d61a7572ddd19d7941e271515c) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add big reformat commits to ignore revs for blame (#2286) * Bump github/codeql-action from 3.25.13 to 3.25.15 (#2288) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.13 to 3.25.15. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/2d790406f505036ef40ecba973cc774a50395aac...afb54ba388a7dca6ecae48f608c4ff05ff4cc77a) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump ossf/scorecard-action from 2.3.3 to 2.4.0 (#2287) Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.3.3 to 2.4.0. - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](https://github.com/ossf/scorecard-action/compare/dc50aa9510b46c811795eb24b2f1ba02a914e534...62b2cac7ed8198b15735ed49ab1e5cf35480ba46) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Sparse - coo2csr: deactivating test on PVC (#2290) * Sparse - coo2csr: deactivating test on PVC With this test deactivated everything in Kokkos Kernels passes. Let us confirm that with a nightly build and potentially create of SYCL CI-build. * Protecting SYCL check with preprocessor guard * cmake: add CMake language support for CUDA/HIP (#2173) * cmake: add CMake language support for CUDA/HIP * Apply suggestions of @brian-kelley * Make sure clang is using a newer GCC on weaver (#2289) It's clear from the name of the AT job GCC930_Light_Tpls_GCC930_Tpls_CLANG13CUDA10 that the intent was to use gcc-9.3 but gcc-7.4.0 was the one actually being used because the clang-13 module loads that gcc. * Bump actions/upload-artifact from 4.3.4 to 4.3.5 (#2295) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.3.4 to 4.3.5. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/0b2256b8c012f0828dc542b3febcab082c67f72b...89ef406dd8d7e03cfd12d9e0a4a378f454709029) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * SpAdd handle: delete sort_option getter/setter (#2296) SpAdd handle was originally a copy-paste of the spgemm handle way back in #122, and included get_sort_option() and set_sort_option() from spgemm. But these try to use the member bool sort_option, which doesn't exist. Somehow these functions never produced compile errors until someone tried to call them. * Add support for BSRs to sptrsv (#2281) * Some cleanup and refactoring * First round of cleanup complete * Fix a couple warnings * formatting * Cleanup progress * Fixes * Remove Upper/Lower TriLvlSchedTP2SolverFunctors * Remove Upper/Lower single block functors * Remove unused TriLvlSchedTP1SingleBlockFunctorDiagValues and merge upper/lower tri_solve_cg * Merge two big upper/lower branch of tri_solve_chain * Merge upper/lower tri_solve_streams * progres * progress * Progress, test added * progress and fixes * prog * prog but broken * Prog with debug prints * Remove extreme debug printing * works * all working * Remove test mangling * Switch over block spiluk precond test to use new block sptrsv * More test cleanup * Fixes for GPU warnings * Conflicts resolved, still work needed * builds * Formatting * Update work to latest format style * Remove unused functions. Remove prints. Add barriers * Minor fixes * lset is not used * Fix for clang * formatting * New impl approach * Unset macro * There's no reason to limit team-policy alg to MAX_VEC_SIZE * formatting * Add missing kokkos-inline-funcs * Fix warnings * format * Some compilers throw shadow warnings in static functions (#2297) * Update Solo GCC version: 10.2.1 -> 10.3.1 (#2300) * github workflow: adding release workflow to have provenance for release artifacts (#2304) This adds a workflow based on the scorecard recommendation for software provenance. The workflow requires some manual actions to verify that the signiture in the release is correct. * Improve crs/bsr sorting performance (#2293) * CRS sorting improvements - Wrote bulk sort/permutation based sorting for CRS graph, matrix, and BSR matrix (bulk = one large sort of all the entries, using row-major dense index as keys) - This is more performant for imbalanced entries per row - If matrix dimensions are too large to do bulk sort, fall back to sorting within each row with a thread. * Add perf test for sort_crs_matrix * sort_crs: improve parallel labels * Work around kokkos issue 7036 * sort_crs: replace radix sort lambda with functor (Lambda segfaults with nvcc+openmp) --------- Signed-off-by: Brian Kelley <[email protected]> * Don't error out if graph unit tests disabled (#2305) Graph unit tests, with TEST_ETI_ONLY=ON, require double and/or float to be enabled as scalars. Instead of erroring out the configure, just give a warning and disable the graph tests. * Update version to 4.4.99 (#2302) * Update version to 4.4.99 Update min kokkos version to 4.3.01 * update workflows yaml files to test with [email protected] * Deprecate redundant team-level sort functions (#2306) * Deprecate redundant team-level sort functions These were moved into Kokkos core a long time ago with a nicer interface and better testing. Replace our implementations with calls to the Kokkos functions like Kokkos::Experimental::sort_team. * Formatting Signed-off-by: Brian Kelley <[email protected]> * Use our own DefaultComparator, not use Kokkos impl --------- Signed-off-by: Brian Kelley <[email protected]> * Bump actions/upload-artifact from 4.3.5 to 4.3.6 (#2307) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.3.5 to 4.3.6. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/89ef406dd8d7e03cfd12d9e0a4a378f454709029...834a144ee995460fba8ed112a2fc961b36a5ec5a) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump step-security/harden-runner from 2.9.0 to 2.9.1 (#2309) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.9.0 to 2.9.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/0d381219ddf674d61a7572ddd19d7941e271515c...5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.25.15 to 3.26.0 (#2308) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.25.15 to 3.26.0. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/afb54ba388a7dca6ecae48f608c4ff05ff4cc77a...eb055d739abdc2e8de2e5f4ba1a8b246daa779aa) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Eti extern marking (#2292) * ETI: adding headers for template instantiation declarations * ETI: adding more decl files to eti Now all the sparse kernels have an ETI decl file to prevent multiple template instantiation. * ETI: adding BLAS kernels that are called from Sparse kernels. * Fixing CMAKE logic * clang-format * ETI work: finish the declarations for BLAS and adding GRAPH, LAPACK and BATCHED * clang-format * Fixing two headers and rename Nrm2w<2-D> as Nrm2w_mv * update changelog for 4.4.00 (#2310) * Bump github/codeql-action from 3.26.0 to 3.26.2 (#2311) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.0 to 3.26.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/eb055d739abdc2e8de2e5f4ba1a8b246daa779aa...429e1977040da7a23b6822b13c129cd1ba93dbb2) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Restore size_t as default offset, in Tribits builds (#2313) If building KokkosKernels standalone, leave int as the default offset (this was the case since #2140). But if building KokkosKernels as a Trilinos/Tribits package, then make size_t the default offset because this is what the Tpetra stack currently uses. Signed-off-by: Brian Kelley <[email protected]> * Improve GH action to produce release artifacts (#2312) * Fix minor typing error. (#2314) * Bump github/codeql-action from 3.26.2 to 3.26.5 (#2315) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.2 to 3.26.5. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/429e1977040da7a23b6822b13c129cd1ba93dbb2...2c779ab0d087cd7fe7b826087247c2c81f27bfa6) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Implement batched serial pttrs (#2277) * Implement batched serial pttrs * Add tests for pttrs * Add tag for pttrs * fix: remove unnecessary specialization for pttrs internal * format * format --------- Co-authored-by: Yuuichi Asahi <[email protected]> * .github/workflows: Group jobs under common github-AT2 name (#2320) * coo2csr: add parens to function calls (#2318) * Bump github/codeql-action from 3.26.5 to 3.26.6 (#2323) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.5 to 3.26.6. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/2c779ab0d087cd7fe7b826087247c2c81f27bfa6...4dd16135b69a43b6c8efb853346f8437d92d3c93) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/upload-artifact from 4.3.6 to 4.4.0 (#2324) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.3.6 to 4.4.0. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/834a144ee995460fba8ed112a2fc961b36a5ec5a...50769540e7f4bd5e21e526ee35c689e35e0d6874) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add MAGMA TPL support for GESV on HIP backend (#2326) * Small changes for MAGMA GESV on HIP * Apply clang-format * Relax eps to 1e-8 for multi-rhs tests --------- Co-authored-by: Vinh Quang Dang (-EXP) <[email protected]> * implement batched serial pbtrf (#2322) * implement batched serial pbtrf * fix: docstring * Add tests for info * fix CodeQL * fix: type * Add a analytical test case for pbtrf --------- Co-authored-by: Yuuichi Asahi <[email protected]> * remove unneeded volatile qualifier for Kokkos::Single (#2333) * AT-2: adding non-TPL build for HIP backend (#2329) * AT-2: adding non-TPL build for HIP backend Clean-up a few things in the mi210 workflow as well should make it a little bit more readable and maintainable. * AT-2: updating hip no tpl runs-on tag By reusing the same tag this should allow the job to run without issues with the same runner as the tpl job. * removing tabs and putting whitespaces instead * hopefully fixing paths in mi210.yml * AT-2: using env variable to get abs path, let's see... * replacing tabs with whitespaces * AST-2: Fixing mkdir? * removing a tab... * Fix typo in working-directory for kokkos build step * another fix to a path * Fixing quotation... * Fixing working-dir which is already in $GITHUB_WORKSPACE * fixing path in the kokkos-kernels configure step * Fixing configure step for tpl build * Bump github/codeql-action from 3.26.6 to 3.26.7 (#2338) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.6 to 3.26.7. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/4dd16135b69a43b6c8efb853346f8437d92d3c93...8214744c546c1e5c8f03dde8fab3a7353211988d) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump step-security/harden-runner from 2.9.1 to 2.10.1 (#2339) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.9.1 to 2.10.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/5c7944e73c4c2a096b17a9cb74d65b6c2bbafbde...91182cccc01eb5e619899d80e4e971d6181294a7) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update changelog for 4.4.01 (#2340) * Bump github/codeql-action from 3.26.7 to 3.26.8 (#2343) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.7 to 3.26.8. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/8214744c546c1e5c8f03dde8fab3a7353211988d...294a9d92911152fe08befb9ec03e240add280cb3) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.26.8 to 3.26.9 (#2348) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.8 to 3.26.9. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/294a9d92911152fe08befb9ec03e240add280cb3...461ef6c76dfe95d5c364de2f431ddbd31a417628) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * .github/workflows: Add remaining spr and bdw checks (#2321) * .github/workflows: Add llvm1001 and inteloneapi AT2 checks * .github/workflows: Enable gcc10 AT2 builds * .github/workflows: Stage volta70 checks * .github/workflows: Test spr against kokkos 4.3.01 * .github/workflows: Specify ETI types for spr * .github/workflows: Disable two of the GNU1020 builds * Add KokkosKernels::eager_initialize() to common (#2317) * Add KokkosKernels::eager_initialize() to common * Formatting * TPL singletons: allow query of whether initialized And test KokkosKernels::eager_initialize() using this * Fix magma build - build TPL singleton file into library when magma's enabled - include correct magma TPL header with declarations, not definitions * Modify validity checks for output views sizes in svd (#2350) * Modify validity check for output views sizes in svd * Apply clang format * Apply clang format * kk_is_gpu_exec_space() -> is_gpu_exec_space_v (#2354) * Fix #2344: SVD hanging (#2345) * Fix #2344: hang in SerialSVD Add test for the case that failed. * Add more SVD tests to exercise corner cases Used temporary printfs in the two zero-diagonal codepaths to make sure they are now covered by testing * Revert replacing spadd example with reproducer * Clean up debug printouts * Fix -Wshadow * SVD: Add more rank-deficient test cases * Last fix for SVD, test cleanup * SVD test fixes * Comment both test cases from issue 2344 * workflow: adding permissions in workflow files (#2357) This should make the OSS scorecard a little happier? Signed-off-by: Luc <[email protected]> * Bypass bulk sort in KokkosSparse::sort_crs_matrix sometimes (#2353) * set [[maybe_unused]] attribute on mySys (#2355) * Fix compilation error, kk_is_gpu_exec_space->is_gpu_exec_space_v (#2358) Apply change consistent with PR #2354 * Bump github/codeql-action from 3.26.9 to 3.26.11 (#2360) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.9 to 3.26.11. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/461ef6c76dfe95d5c364de2f431ddbd31a417628...6db8d6351fd0be61f9ed8ebd12ccd35dcec51fea) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * sparse_sort_crs: fix column shuffle indices (#2346) * random_shuffle -> shuffle random_shuffle is deprecated / removed * sparse_sort_crs: Fix row begin/end offset in entry shuffle * workflows: fixing some action versions using current sha (#2361) * Bump actions/checkout from 4.1.7 to 4.2.1 (#2363) Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.7 to 4.2.1. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/692973e3d937129bcbf40652eb9f2f61becf3332...eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * workflow: update the documentation workflow to use pinned python modules (#2366) * Workflow volta70 (#2356) * worflow - volta70: cleaning up cmake recipes * Adding volta70 to at2.yml * gemm perf_test: print matrix sizes (#2362) * workflows: fixing dependency for checkout action to make dependabot happy (#2369) Signed-off-by: Luc <[email protected]> * workflows: limit the permissions in volta70 build (#2370) Reducing the permissions keeps the workflow and repository safe from potential malicious deeds. Signed-off-by: Luc Berger-Vergiat <[email protected]> * OpenMPSmartStatic_SPMV.hpp: throw if posix_memalign fails (#2368) * Bump actions/upload-artifact from 4.4.0 to 4.4.3 (#2378) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.4.0 to 4.4.3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/50769540e7f4bd5e21e526ee35c689e35e0d6874...b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump github/codeql-action from 3.26.11 to 3.26.12 (#2377) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.11 to 3.26.12. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/6db8d6351fd0be61f9ed8ebd12ccd35dcec51fea...c36620d31ac7c881962c3d9dd939c40ec9434f2b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * set KokkosKernels_ENABLE_COMPONENT variables to value instead of variable name (#2380) Signed-off-by: Carl Pearson <[email protected]> * Block Sptrsv fixes (#2376) * Go back to original impl with vector reduce Signed-off-by: James Foucar <[email protected]> * Disable tp1 test for clang+cuda+complex Signed-off-by: James Foucar <[email protected]> * Fixes and warn users about broken case Signed-off-by: James Foucar <[email protected]> * formatting Signed-off-by: James Foucar <[email protected]> * Fix comments and print skip message Signed-off-by: James Foucar <[email protected]> --------- Signed-off-by: James Foucar <[email protected]> * Do not specify template argument when using Kokkos atomics (#2382) Let Function Template Argument Deduction do its job, do not interfere. Signed-off-by: Damien L-G <[email protected]> * Blas1 asum: work around for openblas error with short vectors (#2384) Signed-off-by: Carl William Pearson <[email protected]> * Prefer atomic_assign(ptr, val) -> atomic_store(ptr, val) (#2383) We are looking at deprecating atomic_assign() https://github.com/kokkos/kokkos/issues/7449 Use atomic_store() instead. Signed-off-by: Damien L-G <[email protected]> * search/replace KOKKOS_-prefixed macros (#2372) Signed-off-by: Carl Pearson <[email protected]> * Replace atomic_{inc, dec}[rement] (#2386) Signed-off-by: Damien L-G <[email protected]> * put default types in KokkosKernels namespace (#2341) * put default types in KokkosKernels namespace Signed-off-by: Carl Pearson <[email protected]> * Deprecate global namespace default type aliases Signed-off-by: Carl Pearson <[email protected]> --------- Signed-off-by: Carl Pearson <[email protected]> * perf_tests: remove false dependence on google test (#2385) * perf_tests: remove false dependence on google test Signed-off-by: Carl Pearson <[email protected]> * KokkosBlas3_gemm_perf_test.hpp: remove comment Signed-off-by: Carl Pearson <[email protected]> * Test::epsilon -> Kokkos::ArithTraits<>::eps Signed-off-by: Carl Pearson <[email protected]> --------- Signed-off-by: Carl Pearson <[email protected]> * Prefer `expected == atomic_compare_exchange(ptr, expected, desired)` (#2387) * Prefer expected == atomic_compare_exchange(ptr, expected, desired) Signed-off-by: Damien L-G <[email protected]> * Reintroduce break statement that was accidentally removed Signed-off-by: Damien L-G <[email protected]> --------- Signed-off-by: Damien L-G <[email protected]> * workflows: adding variable to set kokkos version to test against (#2389) * workflows: adding variable to set kokkos version to test against The variable is set directly in at2.yml so it can be uniformly applied to all the "sub-workflows" making maintenance when a new release of kokkos comes out easier. Signed-off-by: Luc Berger-Vergiat <[email protected]> * workflow: fix for the osx builds The new variable to set the version of Kokkos Core to build against needs to use the "in script syntax" not the bash syntax. Signed-off-by: Luc Berger-Vergiat <[email protected]> --------- Signed-off-by: Luc Berger-Vergiat <[email protected]> * Bump github/codeql-action from 3.26.12 to 3.26.13 (#2391) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.12 to 3.26.13. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/c36620d31ac7c881962c3d9dd939c40ec9434f2b...f779452ac5af1c261dce0346a8f964149f49322b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * remove deprecation message on intel 19 (#2393) Signed-off-by: Carl Pearson <[email protected]> * deprecate `__KOKKOSBATCHED_PROMOTION__` (#2392) * deprecate __KOKKOSBATCHED_PROMOTION__ Signed-off-by: Carl Pearson <[email protected]> * __KOKKOSBATCHED_PROMOTION___DEPRECATED_MACRO -> KOKKOSBATCHED_IMPL_PROMOTION Signed-off-by: Carl Pearson <[email protected]> --------- Signed-off-by: Carl Pearson <[email protected]> * Reduce duplicated code in trsv (#2388) * Reduce duplicated code in trsv A slightly different for loop can avoid having to separate out the last iteration. * Fix inner loops underflow * Change to a more-readable loop Signed-off-by: James Foucar <[email protected]> * Implement batched serial laswp (#2395) * Implement batched serial laswp Signed-off-by: Yuuichi Asahi <[email protected]> * fix: integer types in laswp test Signed-off-by: Yuuichi Asahi <[email protected]> * change loop order based on base layout Signed-off-by: Yuuichi Asahi <[email protected]> * update serial laswp test based on review Signed-off-by: Yuuichi Asahi <[email protected]> --------- Signed-off-by: Yuuichi Asahi <[email protected]> Co-authored-by: Yuuichi Asahi <[email protected]> * 2392 missed a case where __KOKKOSBATCHED_PROMOTION__ was defined (#2396) Signed-off-by: Carl Pearson <[email protected]> * Rename reserved identifiers (#2373) * clang-tidy file for reserved identifiers Signed-off-by: Carl Pearson <[email protected]> * Batched: don't use reserved names in include guards Signed-off-by: Carl Pearson <[email protected]> * BLAS: don't use reserved names in include guards Signed-off-by: Carl Pearson <[email protected]> --------- Signed-off-by: Carl Pearson <[email protected]> * implement batched serial pbtrs (#2330) * implement …
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Add a simple perf test for sort_crs_matrix too, but as this isn't needed very often, the CMake to enable it is commented out.
*takes the imbalanced/long row path
The new long row implementation could still be improved. If a matrix has a mixture of long and short rows, it would be better
to use the thread-sort for short rows and the bulk (or possibly a team-level) sort for the long rows. The tradeoff is that it's somewhat more complex to implement than what is in this PR.