Issue 1330 - Deprecate Kokkos abstractions

[Rohit-Kakodkar]

Description

Please describe the changes/features in this pull request.

• Removes kokkos abstractions - wrappers to kokkos functions

Issue Number

If there is an issue created for these changes, link it here

Checklist

Please make sure to check developer documentation on specfem docs.

• I ran the code through pre-commit to check style
• THE DOCUMENTATION BUILDS WITHOUT WARNINGS/ERRORS
• I have added labels to the PR (see right hand side of the PR page)
• My code passes all the integration tests
• I have added sufficient unittests to test my changes
• I have added/updated documentation for the changes I am proposing
• I have updated CMakeLists to ensure my code builds
• My code builds across all platforms

[Copilot]

Pull request overview

This PR removes the project-specific kokkos_abstractions layer and replaces usages with direct Kokkos types and utilities, while simplifying field synchronization APIs and cleaning up legacy testing helpers.

Changes:

• Remove include/kokkos_abstractions.h and all specfem::kokkos view typedefs in favor of explicit Kokkos::View and Kokkos::TeamPolicy / MDRangePolicy usage across core and tests.
• Update assembly, mesh, IO, sources/receivers, and quadrature code to use new Kokkos types and retain host/device mirror support through Kokkos::create_mirror_view and new copy helpers (copy_to_host / copy_to_device).
• Delete legacy unit-test array comparison utilities (compare_array.hpp/.tpp, utilities/include/interface.hpp, and compare_arrays CMake target) and update affected tests to work without them.

Notable Issues

1. Layout mismatch in seismogram test helpers (compile-time type incompatibility)

   • In both tests/unit-tests/seismogram/elastic/seismogram_tests.cpp and tests/unit-tests/seismogram/acoustic/seismogram_tests.cpp, read_field is now declared as:

     void read_field(
         const std::string filename,
         Kokkos::View<type_real **, Kokkos::LayoutRight, Kokkos::HostSpace> &field,
         const int n1, const int n2);

   • The simulation fields expose host views via field_impl as:

     Kokkos::View<type_real **, Kokkos::LayoutLeft, Kokkos::HostSpace>
     field_impl::get_host_field() const;
     // analogous for get_host_field_dot, get_host_field_dot_dot

     (see core/specfem/assembly/fields/impl/field_impl.hpp around get_host_field).
   • The tests pass assembly.fields.forward.elastic.h_field / .h_field_dot / .h_field_dot_dot into read_field. These host field views are consistent with get_host_field*() and thus are LayoutLeft, not LayoutRight.
   • This is a compile-time type mismatch: a Kokkos::View<..., LayoutLeft, HostSpace> cannot bind to a Kokkos::View<..., LayoutRight, HostSpace>&.
   • Suggestion (mandatory): Change read_field’s parameter to use Kokkos::LayoutLeft (or, better, template on the layout and memory space to accept the exact type from the fields), e.g.:
     • Kokkos::View<type_real **, Kokkos::LayoutLeft, Kokkos::HostSpace> &field, or
     • a template template <class ViewType> void read_field(..., ViewType &field, ...) with appropriate static_assert on rank.

2. Minor type alias inconsistency in compute_tests.cpp (optional clean-up)

   • In tests/unit-tests/assembly_mesh/index/compute_tests.cpp, the aliases

     using HostView1d =
         Kokkos::View<type_real *, Kokkos::LayoutRight, Kokkos::HostSpace>;
     using HostView2d =
         Kokkos::View<type_real **, Kokkos::LayoutRight, Kokkos::HostSpace>;
     using HostView3d =
         Kokkos::View<type_real ***, Kokkos::LayoutRight, Kokkos::HostSpace>;

     are defined but never used in the file.
   • On main, these aliases referred to integer-index views (HostView{1,2,3}d<int>), matching their semantic use; changing them to type_real is misleading even though they are currently unused.
   • Suggestion (optional, maintainability): Either remove these unused aliases or restore them to int to match their intended purpose, to avoid confusion for future readers.

Reviewed changes

Copilot reviewed 130 out of 130 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/unit-tests/utilities/src/compare_array.cpp	Removes dependency on kokkos_abstractions.h and legacy interface, leaving only basic equate helpers and commented-out array comparison code.
tests/unit-tests/utilities/include/interface.hpp	Deletes the unit-test header that only re-exported compare_array utilities.
tests/unit-tests/utilities/include/compare_array.tpp	Removes template implementation of array comparison utilities that depended on specfem::kokkos views.
tests/unit-tests/utilities/include/compare_array.hpp	Removes array comparison template declarations based on specfem::kokkos host views.
tests/unit-tests/source_time_function/source_time_function_tests.cpp	Replaces specfem::kokkos::HostView2d with explicit Kokkos::View<..., LayoutRight, HostSpace> for STF arrays in multiple tests.
tests/unit-tests/source/source.hpp	Drops unused include of kokkos_abstractions.h from source tests.
tests/unit-tests/source/dim3/vector_sources/force_source.hpp	Switches specfem::kokkos::HostView1d force vectors to explicit 1D Kokkos::View in host memory.
tests/unit-tests/source/dim3/tensor_sources/moment_tensor_source.hpp	Switches 2D specfem::kokkos::HostView2d source tensors to explicit Kokkos::View host views.
tests/unit-tests/source/dim2/vector_sources/force_source.hpp	Uses explicit 1D Kokkos::View for 2D vector source force arrays instead of HostView1d.
tests/unit-tests/source/dim2/vector_sources/external_source.hpp	Same as above for external 2D sources: replaces HostView1d with Kokkos::View on host.
tests/unit-tests/source/dim2/vector_sources/cosserat_force_source.hpp	Same as above for Cosserat force sources, replacing HostView1d.
tests/unit-tests/source/dim2/vector_sources/adjoint_source.hpp	Same as above for adjoint sources, replacing HostView1d.
tests/unit-tests/source/dim2/tensor_sources/moment_tensor_source.hpp	Replaces HostView2d for moment tensor source arrays by Kokkos::View host views.
tests/unit-tests/seismogram/elastic/seismogram_tests.cpp	Changes read_field to take a 2D LayoutRight host Kokkos::View and uses new assembly.fields.copy_to_device(); introduces the layout mismatch issue described above.
tests/unit-tests/seismogram/acoustic/seismogram_tests.cpp	Same read_field change as elastic tests, with same layout mismatch concern.
tests/unit-tests/jacobian/dim3/compute_locations_tests.cpp	Removes unused kokkos_abstractions.h include from 3D Jacobian location tests.
tests/unit-tests/jacobian/dim3/compute_jacobian_tests.cpp	Removes unused kokkos_abstractions.h include from 3D Jacobian tests.
tests/unit-tests/jacobian/dim2/compute_locations_tests.cpp	Removes unused kokkos_abstractions.h include from 2D Jacobian location tests.
tests/unit-tests/jacobian/dim2/compute_jacobian_tests.cpp	Removes unused kokkos_abstractions.h include from 2D Jacobian tests.
tests/unit-tests/gll/gll_tests.cpp	Replaces specfem::kokkos::{DeviceView1d,HostMirror1d} with concrete Kokkos::View types parameterized by DefaultExecutionSpace::memory_space and HostSpace.
tests/unit-tests/displacement_tests/Newmark/dim3/newmark_tests.cpp	Drops dependency on the deleted utilities/include/interface.hpp.
tests/unit-tests/displacement_tests/Newmark/dim2/newmark_tests.cpp	Same as above for 2D Newmark tests.
tests/unit-tests/assembly_mesh/jacobian_matrix/compute_jacobian_matrix_tests.cpp	Drops interface.hpp include, leaving test to use core assembly/jacobian APIs directly.
tests/unit-tests/assembly_mesh/index/compute_tests.cpp	Drops interface.hpp include and updates type aliases to raw Kokkos::View; also switches MDRangePolicy to plain Kokkos (no specfem::kokkos::HostMDrange).
tests/unit-tests/assembly/mesh/utilities.cpp	Replaces specfem::kokkos::HostView4d with explicit 4D host Kokkos::View for mesh coordinate construction in tests.
tests/unit-tests/assembly/compute_source_array/dim3/compute_source_array_from_vector.cpp	Removes unused kokkos_abstractions.h include from 3D vector source array tests.
tests/unit-tests/assembly/compute_source_array/dim3/compute_source_array_from_tensor.cpp	Removes unused kokkos_abstractions.h include from 3D tensor source array tests.
tests/unit-tests/assembly/compute_source_array/dim2/compute_source_array_from_vector.cpp	Removes unused kokkos_abstractions.h include from 2D vector source array tests.
tests/unit-tests/assembly/compute_source_array/dim2/compute_source_array_from_tensor.cpp	Removes unused kokkos_abstractions.h and switches Jacobian test array to Kokkos::View.
tests/unit-tests/algorithms/locate.cpp	Replaces specfem::kokkos-based host views and team policy with plain Kokkos View and TeamPolicy<DefaultHostExecutionSpace> for 2D point-location tests.
tests/unit-tests/algorithms/dim3/locate_point_fixture.cpp	Removes kokkos_abstractions.h include from 3D locate-point fixtures.
tests/unit-tests/algorithms/dim2/locate_point_fixture.hpp	Removes kokkos_abstractions.h include from 2D locate-point fixtures.
tests/unit-tests/CMakeLists.txt	Deletes the compare_arrays utility library target and its linkage from affected tests.
include/kokkos_abstractions.h	Entire file removed; project now relies on direct Kokkos APIs and the new specfem::kokkos in domain_view.hpp for chunked domain views only.
include/enumerations/specfem_enums.hpp	Removes unnecessary include of kokkos_abstractions.h.
core/specfem/source_time_functions/source_time_function.hpp	Drops dependency on kokkos_abstractions.h; keeps direct Kokkos_Core.hpp include.
core/specfem/source_time_functions/gaussianhdur.hpp	Removes kokkos_abstractions.h include.
core/specfem/source_time_functions/gaussian.hpp	Removes kokkos_abstractions.h include.
core/specfem/source_time_functions/external.hpp	Removes kokkos_abstractions.h include; still uses enumerations and base STF APIs.
core/specfem/source_time_functions/external.cpp	Drops kokkos_abstractions.h include.
core/specfem/source_time_functions/dirac.hpp	Removes kokkos_abstractions.h include.
core/specfem/source/tensor_source.hpp	Removes kokkos_abstractions.h include from tensor source interface.
core/specfem/source/source.tpp	Cleans up includes (removes kokkos_abstractions.h) and rewraps long make_unique calls for clarity.
core/specfem/source/source.hpp	Removes kokkos_abstractions.h include from source interface.
core/specfem/source/dim3/vector_source/force_source.hpp	Removes kokkos_abstractions.h include from 3D force source header.
core/specfem/source/dim3/tensor_source/moment_tensor_source.hpp	Removes kokkos_abstractions.h include from 3D tensor source header.
core/specfem/source/dim3/tensor_source/moment_tensor_source.cpp	Drops kokkos_abstractions.h include from 3D moment tensor implementation.
core/specfem/source/dim3/source.tpp	Removes kokkos_abstractions.h include and reflows template constructor code.
core/specfem/source/dim3/source.cpp	Removes kokkos_abstractions.h include from 3D source implementation.
core/specfem/source/dim2/vector_source/force_source.hpp	Removes kokkos_abstractions.h include from 2D force source header.
core/specfem/source/dim2/vector_source/external.hpp	Removes kokkos_abstractions.h include from 2D external source header.
core/specfem/source/dim2/vector_source/cosserat_force_source.hpp	Removes kokkos_abstractions.h include from Cosserat source header.
core/specfem/source/dim2/vector_source/adjoint_source.hpp	Removes kokkos_abstractions.h include from adjoint source header.
core/specfem/source/dim2/tensor_source/moment_tensor_source.hpp	Removes kokkos_abstractions.h include and adjusts doc comment wording.
core/specfem/source/dim2/tensor_source/moment_tensor_source.cpp	Drops kokkos_abstractions.h include from 2D moment tensor implementation.
core/specfem/source/dim2/source.tpp	Removes kokkos_abstractions.h include and reflows constructor template.
core/specfem/source/dim2/source.cpp	Removes kokkos_abstractions.h include from 2D source implementation.
core/specfem/receivers/dim3/receiver.hpp	Removes kokkos_abstractions.h include from 3D receiver header.
core/specfem/receivers/dim3/receiver.cpp	Drops kokkos_abstractions.h include from 3D receiver implementation.
core/specfem/receivers/dim2/receiver.hpp	Removes kokkos_abstractions.h include from 2D receiver header.
core/specfem/receivers/dim2/receiver.cpp	Drops kokkos_abstractions.h include from 2D receiver implementation.
core/specfem/quadrature/quadrature.hpp	Removes kokkos_abstractions.h include; keeps direct Kokkos usage.
core/specfem/quadrature/gll/lagrange_poly.hpp	Removes kokkos_abstractions.h include.
core/specfem/quadrature/gll/gll_utils.hpp	Removes kokkos_abstractions.h include.
core/specfem/quadrature/gll/gll_utils.cpp	Drops kokkos_abstractions.h include from GLL utilities implementation.
core/specfem/quadrature/gll/gll_library.hpp	Removes kokkos_abstractions.h include.
core/specfem/quadrature/gll/gll.hpp	Removes kokkos_abstractions.h include from core GLL interface.
core/specfem/quadrature/gll/gll.cpp	Drops kokkos_abstractions.h include from GLL implementation.
core/specfem/program/program.cpp	Drops kokkos_abstractions.h include from main program driver.
core/specfem/mesh/dim2/tags/tags.cpp	Removes kokkos_abstractions.h include from 2D tags implementation.
core/specfem/mesh/dim2/mpi_interfaces/mpi_interfaces.hpp	Removes unused kokkos_abstractions.h include.
core/specfem/mesh/dim2/mesh.cpp	Drops kokkos_abstractions.h include and updates knods to a host Kokkos::View<int **, LayoutRight, DefaultHostExecutionSpace>.
core/specfem/mesh/dim2/materials/materials.hpp	Removes kokkos_abstractions.h include from 2D materials header.
core/specfem/mesh/dim2/elements/tangential_elements.hpp	Removes unused kokkos_abstractions.h include.
core/specfem/mesh/dim2/elements/axial_elements.hpp	Removes unused kokkos_abstractions.h include.
core/specfem/mesh/dim2/control_nodes/control_nodes.hpp	Removes kokkos_abstractions.h include from control nodes header.
core/specfem/mesh/dim2/boundaries/forcing_boundaries.hpp	Removes unused kokkos_abstractions.h include.
core/specfem/jacobian/dim3/jacobian.hpp	Removes kokkos_abstractions.h include from 3D jacobian header.
core/specfem/jacobian/dim2/jacobian.hpp	Removes kokkos_abstractions.h include from 2D jacobian header.
core/specfem/jacobian.hpp	Drops kokkos_abstractions.h include from jacobian front-end header.
core/specfem/io/seismogram/reader.hpp	Replaces specfem::kokkos::HostView2d with explicit Kokkos::View<type_real **, LayoutRight, DefaultHostExecutionSpace> for source-time-function storage.
core/specfem/io/property/reader.tpp	Removes kokkos_abstractions.h and reflows FOR_EACH_IN_PRODUCT arguments for properties reading.
core/specfem/io/mesh/impl/fortran/dim2/read_mesh_database.hpp	Replaces specfem::kokkos::HostView2d return type with 2D host Kokkos::View for coordinate arrays.
core/specfem/io/mesh/impl/fortran/dim2/read_mesh_database.cpp	Implements read_coorg_elements using explicit 2D host Kokkos::View instead of HostView2d.
core/specfem/io/mesh/impl/fortran/dim2/read_material_properties.hpp	Updates knods parameter type to a 2D host Kokkos::View<int **, LayoutRight, DefaultHostExecutionSpace>.
core/specfem/io/mesh/impl/fortran/dim2/read_material_properties.cpp	Propagates new knods and material_index_mapping view types (Kokkos::View<..., LayoutRight, DefaultHostExecutionSpace>) in material reading and index assignment.
core/specfem/io/mesh/impl/fortran/dim2/read_boundaries.cpp	Rewrites boundary helper functions to use only Kokkos View/Subview on DefaultHostExecutionSpace instead of specfem::kokkos views.
core/specfem/io/mesh/impl/fortran/dim2/mesh.cpp	Updates mesh.control_nodes.knods to a Kokkos::View<int **, LayoutRight, DefaultHostExecutionSpace> and removes kokkos_abstractions.h.
core/specfem/io/impl/medium_writer.tpp	Removes kokkos_abstractions.h usage, switches to DomainView2d alias, and simplifies element index host extraction.
core/specfem/io/NPZ/impl/dataset.tpp	Removes specfem::kokkos::HostMemSpace/DevMemSpace in favor of direct Kokkos::HostSpace and DefaultExecutionSpace::memory_space checks for view memory space.
core/specfem/io/NPY/impl/dataset.tpp	Same memory-space simplification as NPZ datasets.
core/specfem/io/HDF5/impl/dataset.tpp	Same memory-space simplification as NPZ/NPY datasets.
core/specfem/io/ASCII/impl/dataset.tpp	Same memory-space simplification as NPZ/NPY datasets.
core/specfem/io/ADIOS2/impl/dataset.tpp	Same memory-space simplification and formatting of ADIOS2 dataset I/O path.
core/specfem/assembly/sources/dim3/sources.cpp	Removes kokkos_abstractions.h and depends only on core Kokkos APIs for sources assembly.
core/specfem/assembly/sources/dim2/sources.cpp	Same as above for 2D sources.
core/specfem/assembly/receivers/dim3/receivers.cpp	Removes kokkos_abstractions.h include, retaining pure Kokkos-based receivers assembly.
core/specfem/assembly/receivers/dim2/receivers.cpp	Same as above for 2D receivers.
core/specfem/assembly/properties/dim3/properties.hpp	Removes kokkos_abstractions.h include from 3D properties header.
core/specfem/assembly/properties/dim2/properties.hpp	Removes kokkos_abstractions.h include from 2D properties header.
core/specfem/assembly/mesh/dim3/mesh.hpp	Removes kokkos_abstractions.h include from 3D assembly mesh header.
core/specfem/assembly/mesh/dim2/mesh.tpp	Drops kokkos_abstractions.h, updates includes ordering, and uses host Kokkos::View in assign_numbering and adjacency graph routines.
core/specfem/assembly/mesh/dim2/impl/utilities.hpp	Replaces kokkos_abstractions.h with basic specfem_setup.hpp and standard headers.
core/specfem/assembly/jacobian_matrix/dim2/jacobian_matrix.hpp	Removes kokkos_abstractions.h include; public API still uses Kokkos views for Jacobian fields.
core/specfem/assembly/jacobian_matrix/dim2/jacobian_matrix.cpp	Keeps use of specfem::kokkos::create_mirror_view / deep_copy (from domain_view.hpp) while dropping kokkos_abstractions.h.
core/specfem/assembly/impl/domain_properties.hpp	Replaces specfem::kokkos::HostView1d<int> with Kokkos::View<int *, LayoutRight, DefaultHostExecutionSpace> for property index mappings.
core/specfem/assembly/impl/domain_properties.tpp	Same replacement in 2D and 3D domain properties constructors and formatting improvements.
core/specfem/assembly/impl/domain_kernels.hpp	Same replacement for domain kernel property index mapping views.
core/specfem/assembly/fields/impl/field_impl.hpp	Removes kokkos_abstractions.h, makes base_field use Kokkos::View<..., LayoutLeft, DefaultExecutionSpace>, and replaces templated sync<HostToDevice/DeviceToHost> with explicit copy_to_host / copy_to_device plus host getters (get_host_field*).
core/specfem/assembly/fields/impl/field_impl.tpp	Updates field_impl constructor to call a new assign_assembly_index_mapping helper and drops the sync_fields<sync> function in favor of copy_to_host / copy_to_device.
core/specfem/assembly/fields/impl/assign_assembly_index_mapping.hpp	Removes kokkos_abstractions.h and ensures only Kokkos and assembly/element_types headers are included.
core/specfem/assembly/fields/dim3/simulation_field.hpp	Replaces sync_fields-based copy helpers with copy_to_host / copy_to_device declarations.
core/specfem/assembly/fields/dim3/simulation_field.tpp	Implements copy_to_host/copy_to_device by calling field_impl::copy_to_* for each medium; also updates nglob computation to use core helper.
core/specfem/assembly/fields/dim3/simulation_field.cpp	Removes explicit instantiation and sync_fields template instantiation TU (simulation fields now fully header-only for 3D).
core/specfem/assembly/fields/dim2/simulation_field.hpp	Same pattern as 3D: removes sync-based helpers and declares copy_to_host / copy_to_device.
core/specfem/assembly/fields/dim2/simulation_field.tpp	Implements 2D copy_to_host/copy_to_device via new field_impl methods.
core/specfem/assembly/fields/dim2/simulation_field.cpp	Removes explicit instantiation and sync_fields instantiation TU for 2D fields.
core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_vector.hpp	Removes kokkos_abstractions.h include from compute-source-array helpers.
core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_vector.cpp	Same include cleanup for implementation file.
core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_tensor.hpp	Same include cleanup for tensor version.
core/specfem/assembly/compute_source_array/dim3/impl/compute_source_array_from_tensor.cpp	Same include cleanup for implementation file.
core/specfem/assembly/compute_source_array/dim3/compute_source_array.tpp	Cleans includes and makes template parameter name more conventional; computation logic unchanged.
core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_vector.hpp	Same include cleanup for 2D vector source array helper.
core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_vector.cpp	Same include cleanup for 2D implementation.
core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_tensor.hpp	Same include cleanup for 2D tensor helper.
core/specfem/assembly/compute_source_array/dim2/impl/compute_source_array_from_tensor.cpp	Same include cleanup for 2D tensor implementation.
core/specfem/assembly/compute_source_array/dim2/compute_source_array.tpp	Cleans includes and asserts rank-3 source arrays; logic unchanged.
core/specfem/assembly/compute_source_array.hpp	Removes kokkos_abstractions.h include; interface now uses only Kokkos and assembly headers.
core/specfem/algorithms/interpolate.hpp	Removes kokkos_abstractions.h include from interpolation algorithms.
core/specfem/algorithms/gradient.hpp	Removes kokkos_abstractions.h include; only textual references to specfem::kokkos::array_type remain in static_assert messages.

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[lsawade]

LGTM, we can take care of the conflicts if you don't have time before traveling, just let us know