Openmp and Cupy development

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# Keep GitHub Actions up to date with GitHub's Dependabot...
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#package-ecosystem
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    groups:
+      github-actions:
+        patterns:
+          - "*"  # Group all Actions updates into a single larger pull request
+    schedule:
+      interval: weekly

.github/workflows/conda-setup.yml

@@ -1,6 +1,6 @@
-name: Conda setup
+name: github CI
 
-on: [push, pull_request]
+on: [pull_request, push]
 
 jobs:
   test_conda:
@@ -9,9 +9,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        os: ["ubuntu-latest", "windows-latest"]
-        python-version: ["3.9", "3.11", "3.13"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+
+        # Our meson.build expects that numpy-config is installed but this 
+        # is not available for python < 3.9
+
+        # 2025/06/19: 3.14 causes an error with conda_incubator/setup-miniconda@v3 
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -25,21 +30,32 @@ jobs:
         run: |
           conda env create --name anuga_env --file environments/environment_${{matrix.python-version}}.yml
 
-      - name: Install mingw compilers on Windows
+      - name: Install gcc compilers on Windows
         if: runner.os == 'Windows'
         shell: bash -el {0}
         run: |
-          conda install -c conda-forge -n anuga_env libpython m2w64-toolchain
+           conda install -c conda-forge -n anuga_env gcc_win-64 gxx_win-64
+           # As of 2025/06/19, strange combination of mpi4py, the new compilers and pytest is
+           # causing a segmentation fault on Windows so we uninstall mpi4py
+           # This is a temporary workaround until the issue is resolved.
+           conda uninstall -n anuga_env mpi4py
 
-      - name: Install package
+      - name: Install clang with openmp compiler on macOS
+        if: runner.os == 'macOS'
+        shell: bash -el {0}
+        run: |
+           conda install -c conda-forge -n anuga_env cxx-compiler llvm-openmp
+
+      - name: Install anuga package
         shell: bash -el {0}
         run: |
           conda activate anuga_env
-          pip install --no-build-isolation .
+          pip install --no-build-isolation -v .
 
       - name: Test package
         shell: bash -el {0}
         run: |
           conda activate anuga_env
           cd ..
-          pytest -p no:faulthandler -q --pyargs anuga
+          export OMP_NUM_THREADS=1
+          pytest -p no:faulthandler -rs --pyargs anuga

.github/workflows/python-package.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "develop-meson" ]
+  release:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    # - name: Lint with flake8
+    #   run: |
+    #     # stop the build if there are Python syntax errors or undefined names
+    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -5,6 +5,8 @@
 [#]*#
 *~
 *$
+*.csv
+*.pstat
 *.bak
 .idea/*
 *.kdev4
@@ -15,6 +17,7 @@
 .settings/
 .*.sw[nop]
 .sw[nop]
+*.pstat
 *.c
 *.cpp
 *.tmp

.readthedocs.yaml

@@ -15,6 +15,11 @@ build:
 sphinx:
   configuration: docs/source/conf.py
 
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+#   - epub
+
 # We recommend specifying your dependencies to enable reproducible builds:
 # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:

README.rst

@@ -1,13 +1,19 @@
 
-.. image:: https://badges.gitter.im/gitterHQ/gitter.png
+.. |badge0| image:: https://badges.gitter.im/gitterHQ/gitter.png
     :target: https://app.gitter.im/#/room/#anuga-community:gitter.im
     :alt: Community Chat
 
-.. image:: https://app.travis-ci.com/anuga-community/anuga_core.svg?branch=develop_hackathon
+..
+    |badge1| image:: https://img.shields.io/travis/com/anuga-community/anuga_core/develop_hackathon.svg
     :target: https://app.travis-ci.com/anuga-community/anuga_core
-    :alt: travis ci status
+    :alt: Travis CI Status
+
+.. |badge1| image:: https://github.com/anuga-community/anuga_core/actions/workflows/conda-setup.yml/badge.svg
+    :target: https://github.com/anuga-community/anuga_core/actions/workflows/conda-setup.yml
+    :alt: GitHub Actions Status
 
-.. image:: https://ci.appveyor.com/api/projects/status/x5airjv7eq2u805w/branch/develop_hackathon?svg=true
+.. 
+    |badge2| image:: https://ci.appveyor.com/api/projects/status/x5airjv7eq2u805w/branch/main?svg=true
     :target: https://ci.appveyor.com/project/stoiver/anuga-core-nwgr0
     :alt: appveyor status
 
@@ -31,7 +37,7 @@
     :target: https://anuga.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-|badge0| |badge1| |badge2| |badge3| |badge3| |badge4| |badge5| |badge6| |badge7|
+|badge0| |badge1| |badge3| |badge4| |badge5| |badge6| |badge7|
 
 
 
@@ -103,7 +109,7 @@ ANUGA documentation is available via "read the docs" at
     https://anuga.readthedocs.io 
 
 Also you can obtain help via the old
-`user_manual <https://github.com/anuga-community/anuga_core/raw/main/doc/anuga_user_manual.pdf>`_
+`user_manual <https://dx.doi.org/10.13140/RG.2.2.17267.81446>`_
 
 Also helpful information is available online at
 

anuga/abstract_2d_finite_volumes/generic_domain.py

@@ -241,13 +241,10 @@ def __init__(self,
 
         #-------------------------------
         # Set multiprocessor mode 
-        # 0. orig (original with edge optim)
-        # 1. simd (used for multiprocessor)
-        # 2. openmp (in development)
-        # 3. openacc (in development)
-        # 4. cuda (in development)
+        # 1. openmp (in development)
+        # 2. cuda (in development)
         #-------------------------------    
-        self.set_multiprocessor_mode(0)
+        self.set_multiprocessor_mode(1)
 
         self.processor = processor
         self.numproc = numproc
@@ -749,18 +746,23 @@ def set_multiprocessor_mode(self, multiprocessor_mode= 0):
         """
         Set multiprocessor mode 
 
-        0. original
-        1. simd (used for multiprocessor)
-        2. openmp (in development)
-        3. openacc (in development)
-        4. cuda (in development)
+        1. openmp (in development)
+        2. cuda (in development)
         """
 
-        if multiprocessor_mode in [0,1,2,3,4]:
+        if multiprocessor_mode in [1,2]:
             self.multiprocessor_mode = multiprocessor_mode
         else:
             raise Exception('multiprocessor mode {multiprocessor_mode} not supported')
 
+    def get_multiprocessor_mode(self):
+        """
+        Get multiprocessor mode 
+
+        1. openmp (in development)
+        2. cuda (in development)
+        """
+        return self.multiprocessor_mode 
 
     def set_using_centroid_averaging(self, flag=True):
         """Set flag to use centroid averaging in output
@@ -2164,10 +2166,7 @@ def evolve_one_rk3_step(self, yieldstep, finaltime):
         # self.saxpy_conserved_quantities(2.0/3.0, 1.0/3.0)
 
         # So do this instead!
-        self.saxpy_conserved_quantities(2.0, 1.0)
-        for name in self.conserved_quantities:
-            Q = self.quantities[name]
-            Q.centroid_values[:] = Q.centroid_values / 3.0
+        self.saxpy_conserved_quantities(2.0, 1.0, 3.0)
 
         # Update special conditions
         # self.update_special_conditions()
@@ -2191,12 +2190,15 @@ def backup_conserved_quantities(self):
             Q = self.quantities[name]
             Q.backup_centroid_values()
 
-    def saxpy_conserved_quantities(self, a, b):
+    def saxpy_conserved_quantities(self, a, b, c=None):
 
-        # Backup conserved_quantities centroid values
+        # saxpy conserved_quantities centroid values with backup values
         for name in self.conserved_quantities:
             Q = self.quantities[name]
             Q.saxpy_centroid_values(a, b)
+            if c is not None:
+                Q.centroid_values[:] = Q.centroid_values / c
+
 
     def conserved_values_to_evolved_values(self, q_cons, q_evol):
         """Needs to be overridden by Domain subclass
@@ -2517,42 +2519,6 @@ def centroid_norm(self, quantity, normfunc):
 
         return normfunc(self.quantities[quantity].centroid_values)
 
-    def apply_protection_against_isolated_degenerate_timesteps(self):
-
-        # FIXME (Steve): This should be in shallow_water as it assumes x and y
-        # momentum
-        if self.protect_against_isolated_degenerate_timesteps is False:
-            return
-
-        # FIXME (Ole): Make this configurable
-        if num.max(self.max_speed) < 10.0:
-            return
-
-        # Setup 10 bins for speed histogram
-        from anuga.utilities.numerical_tools import histogram, create_bins
-
-        bins = create_bins(self.max_speed, 10)
-        hist = histogram(self.max_speed, bins)
-
-        # Look for characteristic signature
-        if len(hist) > 1 and hist[-1] > 0 and \
-           hist[4] == hist[5] == hist[6] == hist[7] == hist[8] == 0:
-            # Danger of isolated degenerate triangles
-
-            # Find triangles in last bin
-            # FIXME - speed up using numeric package
-            d = 0
-            for i in range(self.number_of_triangles):
-                if self.max_speed[i] > bins[-1]:
-                    msg = 'Time=%f: Ignoring isolated high ' % self.get_time()
-                    msg += 'speed triangle '
-                    msg += '#%d of %d with max speed = %f' \
-                        % (i, self.number_of_triangles, self.max_speed[i])
-
-                    self.get_quantity('xmomentum').set_values(0.0, indices=[i])
-                    self.get_quantity('ymomentum').set_values(0.0, indices=[i])
-                    self.max_speed[i] = 0.0
-                    d += 1
 
 
 if __name__ == "__main__":

anuga/abstract_2d_finite_volumes/meson.build

@@ -2,22 +2,6 @@
 inc_dir = include_directories('../utilities', incdir_numpy)
 
 
-openmp = dependency('openmp', required: false)
-if openmp.found()
-  if host_machine.system() == 'windows'
-    # On Windows, the mingw compiler does not support OpenMP ATOMIC operations
-    openmp_deps = dependencies
-  else
-    openmp_deps = dependencies + [openmp]
-  endif
-
-else
-  openmp_deps = dependencies
-endif
-
-# FIXME SR: Need to setup dependencies for openacc code
-openacc_deps = dependencies
-
 # Compile the Cython-generated C code and additional C code
 py3.extension_module('mesh_factory_ext',
   sources: ['mesh_factory_ext.pyx'],
@@ -52,35 +36,22 @@ py3.extension_module('pmesh2domain_ext',
   install: true,
 )
 
-py3.extension_module('quantity_ext',
-  sources: ['quantity_ext.pyx'],
-  include_directories: inc_dir,
-  dependencies: dependencies,
-  subdir: 'anuga/abstract_2d_finite_volumes',
-  install: true,
-)
-
 
 py3.extension_module('quantity_openmp_ext',
   sources: ['quantity_openmp_ext.pyx'],
+  c_args : openmp_c_args,
   include_directories: inc_dir,
   dependencies: openmp_deps,
   subdir: 'anuga/abstract_2d_finite_volumes',
   install: true,
 )
 
-py3.extension_module('quantity_openacc_ext',
-  sources: ['quantity_openacc_ext.pyx'],
-  include_directories: inc_dir,
-  dependencies: openacc_deps,
-  subdir: 'anuga/abstract_2d_finite_volumes',
-  install: true,
-)
 
 py3.extension_module('quantity_cuda_ext',
   sources: ['quantity_cuda_ext.pyx'],
+  c_args : openmp_c_args,
   include_directories: inc_dir,
-  dependencies: dependencies,
+  dependencies: openmp_deps,
   subdir: 'anuga/abstract_2d_finite_volumes',
   install: true,
 )

anuga/abstract_2d_finite_volumes/neighbour_mesh.py

@@ -1005,6 +1005,7 @@ def statistics(self, nbins=10):
         hist = histogram(areas, bins)
 
         str =  '------------------------------------------------\n'
+        str += ' Jorge openmp version \n'
         str += 'Mesh statistics:\n'
         str += '  Number of triangles = %d\n' %len(self)
         str += '  Extent [m]:\n'