Python binding ectrans4py

.github/workflows/build-hpc.yml

@@ -0,0 +1,157 @@
+name: build-hpc
+
+# Controls when the action will run
+on:
+
+  # Trigger the workflow on all pushes to main and develop, except on tag creation
+  push:
+    branches:
+    - main
+    - develop
+    tags-ignore:
+    - '**'
+
+  # Trigger the workflow on all pull requests
+  pull_request: ~
+
+  # Allow workflow to be dispatched on demand
+  workflow_dispatch: ~
+
+  # Trigger after public PR approved for CI
+  pull_request_target:
+    types: [labeled]
+
+env:
+  ECTRANS_TOOLS: ${{ github.workspace }}/.github/tools
+  CTEST_PARALLEL_LEVEL: 1
+  CACHE_SUFFIX: v1        # Increase to force new cache to be created
+
+jobs:
+  ci-hpc:
+    name: ci-hpc
+    if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
+
+    strategy:
+      fail-fast: false    # false: try to complete all jobs
+
+      matrix:
+        name:
+          - ac-gpu nvhpc
+          - lumi-g cce
+
+        include:
+          - name: ac-gpu nvhpc
+            site: ac-batch
+            troika_user_secret: HPC_CI_SSH_USER
+            sbatch_options: |
+              #SBATCH --time=00:20:00
+              #SBATCH --nodes=1
+              #SBATCH --ntasks=2
+              #SBATCH --cpus-per-task=32
+              #SBATCH --gpus-per-task=1
+              #SBATCH --mem=200G
+              #SBATCH --qos=dg
+            modules:
+              - cmake
+              - ninja
+              - prgenv/nvidia
+              - hpcx-openmpi/2.14.0-cuda
+              - fftw
+
+          - name: lumi-g cce
+            site: lumi
+            troika_user_secret: LUMI_CI_SSH_USER
+            sbatch_options: |
+              #SBATCH --time=00:20:00
+              #SBATCH --nodes=1
+              #SBATCH --ntasks-per-node=8
+              #SBATCH --gpus-per-task=1
+              #SBATCH --partition=dev-g
+              #SBATCH --account=project_465000527
+            modules:
+              - CrayEnv
+              - PrgEnv-cray
+              - cce/17.0.1
+              - craype-accel-amd-gfx90a
+              - rocm/6.0.3
+              - cray-fftw
+              - buildtools
+            output_dir: /scratch/project_465000527/github-actions/ectrans/${{ github.run_id }}
+            workdir: /scratch/project_465000527/github-actions/ectrans/${{ github.run_id }}
+            cmake_options: -DOpenMP_C_LIB_NAMES=craymp -DOpenMP_CXX_LIB_NAMES=craymp -DOpenMP_Fortran_LIB_NAMES=craymp -DOpenMP_craymp_LIBRARY=craymp
+            ctest_options: -E gpu
+
+
+    runs-on: [self-hosted, linux, hpc]
+    env:
+      GH_TOKEN: ${{ github.token }}
+    steps:
+      - uses: ecmwf-actions/reusable-workflows/ci-hpc-generic@v2
+        with:
+          site: ${{ matrix.site }}
+          troika_user: ${{ secrets[matrix.troika_user_secret] }}
+          sbatch_options: ${{ matrix.sbatch_options }}
+          output_dir: ${{ matrix.output_dir || '' }}
+          workdir: ${{ matrix.workdir || '' }}
+          template_data: |
+            cmake_options:
+              - -DENABLE_MPI=ON
+              - -DENABLE_ACC=ON
+              - -DENABLE_GPU=ON
+              - ${{ matrix.cmake_options || '' }}
+            ctest_options: ${{ matrix.ctest_options || '' }}
+            dependencies:
+              ecmwf/ecbuild:
+                version: develop
+              ecmwf-ifs/fiat:
+                version: develop
+                cmake_options:
+                  - -DENABLE_MPI=ON
+                  - ${{ matrix.cmake_options || '' }}
+          template: |
+            {% for module in "${{ join(matrix.modules, ',') }}".split(',') %}
+              module load {{module}}
+            {% endfor %}
+
+            export CMAKE_TEST_LAUNCHER="srun;-n;1"
+            export DR_HOOK_ASSERT_MPI_INITIALIZED=0
+            BASEDIR=$PWD
+            {% for name, options in dependencies.items() %}
+                mkdir -p {{name}}
+                pushd {{name}}
+                git init
+                git remote add origin ${{ github.server_url }}/{{name}}
+                git fetch origin {{options['version']}}
+                git reset --hard FETCH_HEAD
+                cmake -G Ninja -S . -B build \
+                  {% for name in dependencies %}
+                    {% set org, proj = name.split('/') %}
+                    -D{{proj}}_ROOT=$BASEDIR/{{name}}/installation \
+                  {% endfor %}
+                  {{ options['cmake_options']|join(' ') }}
+                cmake --build build
+                cmake --install build --prefix installation
+                popd
+            {% endfor %}
+            mkdir -p ${{ github.repository }}
+            pushd ${{ github.repository }}
+            git init
+            git remote add origin ${{ github.server_url }}/${{ github.repository }}
+            git fetch origin ${{ github.sha }}
+            git reset --hard FETCH_HEAD
+            popd
+            cmake -G Ninja -S ${{ github.repository }} -B build \
+              {% for name in dependencies %}
+                {% set org, proj = name.split('/') %}
+                -D{{proj}}_ROOT=$BASEDIR/{{name}}/installation \
+              {% endfor %}
+              {{ cmake_options|join(' ') }}
+            cmake --build build
+            ctest --test-dir build --output-on-failure {{ ctest_options }}
+
+            {% for name in dependencies.keys() %}
+              rm -r {{name}}
+            {% endfor %}
+
+            rm -r ${{ github.repository }}
+            rm -r build

.github/workflows/label-public-pr.yml

@@ -0,0 +1,10 @@
+# Manage labels of pull requests that originate from forks
+name: label-public-pr
+
+on:
+  pull_request_target:
+    types: [opened, synchronize]
+
+jobs:
+  label:
+    uses: ecmwf-actions/reusable-workflows/.github/workflows/label-pr.yml@v2

.gitignore

@@ -8,4 +8,4 @@ build/*
 install/*
 env.sh
 *.DS_Store
-
+*.py[co~]

CMakeLists.txt

@@ -16,6 +16,26 @@ find_package( ecbuild 3.4 REQUIRED HINTS ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CUR
 project( ectrans LANGUAGES C CXX Fortran )
 include( ectrans_macros )
 
+# CMake 3.29 adds CMAKE_TEST_LAUNCHER defined either as CMake variable or environment.
+# This launcher is a semi-colon-separted list of arguments that is used to launch serial tasks,
+# and can be defined during the CMake configuration.
+# This is e.g. required for GPU tests that need access to slurm resources:
+#    export CMAKE_TEST_LAUNCHER="srun;-n;1"
+# To run the tests then:
+#    salloc -q <queue> --gpus-per-task=1 -n <nproc>    ctest <ctest-args>
+# Before cmake 3.29 this could only be achieved with CMAKE_CROSSCOMPILING_EMULATOR.
+# This next snippet ensures forward compatibility
+if( ${CMAKE_VERSION} VERSION_LESS "3.29" )
+  if( DEFINED CMAKE_TEST_LAUNCHER )
+    set(CMAKE_CROSSCOMPILING_EMULATOR ${CMAKE_TEST_LAUNCHER})
+  elseif(DEFINED ENV{CMAKE_TEST_LAUNCHER})
+    set(CMAKE_CROSSCOMPILING_EMULATOR $ENV{CMAKE_TEST_LAUNCHER})
+  endif()
+endif()
+if( CMAKE_CROSSCOMPILING_EMULATOR )
+  set( CMAKE_TEST_LAUNCHER ${CMAKE_CROSSCOMPILING_EMULATOR} )
+endif()
+
 set(CMAKE_CXX_STANDARD 17)
 
 ecbuild_enable_fortran( REQUIRED NO_MODULE_DIRECTORY )
@@ -109,6 +129,11 @@ ecbuild_add_option( FEATURE GPU
                     DESCRIPTION "Compile GPU version of ectrans (Requires OpenACC or sufficient OpenMP offloading support)"
                     CONDITION (HAVE_HIP OR HAVE_CUDA) AND (HAVE_ACC OR HAVE_OMP) )
 
+# Check CPU or GPU is enabled, and if not, abort
+if( (NOT HAVE_CPU) AND (NOT HAVE_GPU) )
+  ecbuild_critical("Please enable one or both of the CPU and GPU features")
+endif()
+
 if( HAVE_GPU )
   if( HAVE_ACC )
     set( GPU_OFFLOAD "ACC" )
@@ -142,10 +167,10 @@ ecbuild_add_option( FEATURE GPU_GRAPHS_GEMM
                     CONDITION HAVE_GPU
                     DESCRIPTION "Enable graph-based optimisation of Legendre transform GEMM kernel" )
 
-	    ecbuild_add_option( FEATURE GPU_GRAPHS_FFT
+ecbuild_add_option( FEATURE GPU_GRAPHS_FFT
                     DEFAULT ON
                     CONDITION HAVE_GPU
-		    DESCRIPTION "Enable graph-based optimisation of FFT kernels" )
+                    DESCRIPTION "Enable graph-based optimisation of FFT kernels" )
 
 if( BUILD_SHARED_LIBS )
   set( GPU_STATIC_DEFAULT OFF )
@@ -156,18 +181,32 @@ ecbuild_add_option( FEATURE GPU_STATIC
                     DEFAULT ${GPU_STATIC_DEFAULT}
                     DESCRIPTION "Compile GPU library as static library")
 
+ecbuild_add_option( FEATURE ETRANS
+                    DEFAULT ON
+                    DESCRIPTION "Include Limited-Area-Model Transforms" )
+
+
+ecbuild_add_option( FEATURE ECTRANS4PY
+                    DEFAULT OFF
+		    CONDITION HAVE_ETRANS
+                    DESCRIPTION "Compile ectrans4py interface routines for python binding w/ ctypesForFortran" )
+
+
 ectrans_find_lapack()
 
 ecbuild_add_option( FEATURE TESTS
                     DEFAULT ON
                     DESCRIPTION "Enable unit testing"
-                    REQUIRED_PACKAGES "MPI COMPONENTS Fortran"
-                    CONDITION HAVE_CPU )
+                    REQUIRED_PACKAGES "MPI COMPONENTS Fortran" )
 
-### Add sources and tests
+### Add sources
 include( ectrans_compile_options )
 add_subdirectory( src )
-add_subdirectory( tests )
+
+### Add tests
+if( HAVE_TESTS )
+  add_subdirectory( tests )
+endif()
 
 ### Export
 if( BUILD_SHARED_LIBS )

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include cmake
+exclude MANIFEST.in

README.md

@@ -106,6 +106,28 @@ The benchmark drivers are found in the bin directory.
 A brief description of available command-line arguments can be obtained with e.g.
 ectrans-benchmark-cpu-sp --help
 
+Building `ectrans4py`
+---------------------
+
+The python wheel can be built from the root of the project, assuming above-mentioned variables are defined (`fiat_ROOT` etc...):
+```
+python -m build --wheel
+```
+and then:
+```
+python -m auditwheel
+```
+The built python wheel is then to be found in directory `wheelhouse/` and can be locally installed by pip:
+```
+pip install wheelhouse/ectrans4py-<x.y.z>(...).whl
+```
+The `_skbuild` and `dist` directories can be deleted.
+
+Tests can be run from `tests/test_ectrans4py/`:
+```
+python -m pytest
+```
+
 Reporting Bugs
 ==============
 

VERSION

@@ -1 +1 @@
-1.5.0
+1.5.1

cmake/ectrans_compile_options.cmake

@@ -25,6 +25,9 @@ elseif( CMAKE_Fortran_COMPILER_ID MATCHES "Cray" )
   ecbuild_add_fortran_flags("-hnomessage=878")  # A module named ... has already been directly or indirectly use associated into this scope
   ecbuild_add_fortran_flags("-hnomessage=867")  # Module ... has no public objects declared in the module, therefore nothing can be use associated from the module.
   ecbuild_add_fortran_flags("-M7256")           # An OpenMP parallel construct in a target region is limited to a single thread.
+elseif( CMAKE_Fortran_COMPILER_ID MATCHES "IntelLLVM" )
+  ecbuild_add_fortran_flags("-march=core-avx2 -no-fma" BUILD BIT)
+  ecbuild_add_fortran_flags("-fp-model precise -fp-speculation=safe")
 elseif( CMAKE_Fortran_COMPILER_ID MATCHES "Intel" )
   ecbuild_add_fortran_flags("-march=core-avx2 -no-fma" BUILD BIT)
   ecbuild_add_fortran_flags("-fast-transcendentals -fp-model precise -fp-speculation=safe")

cmake/project_summary.cmake

@@ -35,6 +35,9 @@ ecbuild_info( "    LAPACK_LIBRARIES         : [${LAPACK_LIBRARIES}]" )
     endif()
 ecbuild_info( "FFTW" )
 ecbuild_info( "    FFTW_LIBRARIES           : [${FFTW_LIBRARIES}]" )
+  if( CMAKE_TEST_LAUNCHER )
+ecbuild_info( "CMAKE_TEST_LAUNCHER          : [${CMAKE_TEST_LAUNCHER}]" )
+  endif()
 ecbuild_info( "---------------------------------------------------------" )
 
 

pyproject.toml

@@ -0,0 +1,23 @@
+[project]
+name = "ectrans4py"
+dynamic = ["version"]
+description = "ECTRANS interface for Python"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies=["numpy", "ctypesForFortran<2.0.0"]
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Science/Research',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Operating System :: Unix',
+]
+
+[build-system]
+requires = ["setuptools", "wheel", "scikit-build"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "ectrans4py.__version__"}

setup.py

@@ -0,0 +1,25 @@
+import os
+import ast
+from skbuild import setup
+
+_version_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "VERSION")
+with open(_version_file, "r") as f:
+    __version__ = f.read().strip()
+
+setup(
+    name="ectrans4py",
+    version=__version__,
+    packages=['ectrans4py'],
+    cmake_minimum_required_version="3.13",
+    cmake_args=[
+        '-DENABLE_ETRANS=ON',
+        '-DENABLE_ECTRANS4PY=ON',
+        '-DENABLE_SINGLE_PRECISION=OFF',
+        '-DENABLE_OMP=ON',
+        '-DFFTW_USE_STATIC_LIBS=ON',
+    ],
+    package_dir={"": "src"},
+    cmake_install_dir="src/ectrans4py",
+    setup_requires=["scikit-build", "setuptools"],
+    install_requires=["numpy", "ctypesforfortran==1.1.3"],
+)

src/CMakeLists.txt

@@ -11,3 +11,9 @@ add_subdirectory( programs )
 if( HAVE_TRANSI )
   add_subdirectory(transi)
 endif()
+if( HAVE_ETRANS )
+  add_subdirectory(etrans)
+endif()
+if(HAVE_ECTRANS4PY)
+  add_subdirectory(ectrans4py)
+endif()