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.github/workflows/testing.yml

@@ -1,57 +1,189 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
+name: Test GeoClaw
 
 on:
   push:
     branches: [ "master" ]
   pull_request:
     branches: [ "master" ]
 
+  workflow_dispatch:
+
 permissions:
   contents: read
 
-jobs:
-  build:
+env:
+  CLAW: ${{ github.workspace }}
 
-    runs-on: ubuntu-latest
+jobs:
+  tests:
+    name: >
+      ${{ matrix.os }} - ${{ matrix.toolchain.compiler }} ${{ matrix.build }} - py ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true # Probably want to turn this off for a large matrix
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        build: [debug, opt]
+        python-version: [3.12]
+        toolchain:
+          - {compiler: gcc, version: 14}
+          - {compiler: gcc, version: 15}
+          # - {compiler: intel, version: '2025.0'}
+          # - {compiler: intel-classic, version: '2021.10'}
+          # - {compiler: nvidia-hpc, version: '25.1'} # does not build python
+          # - {compiler: lfortran, version: '0.45.0'} # lfortran not yet supported
+          # - {compiler: flang, version: '20.1.0'} # flang not yet supported
+        # include:
+        #   3.8 does not seem to work.
+        #   - os: ubuntu-latest
+        #     build: opt
+        #     python-version: 3.8
+        #     toolchain: {compiler: gcc, version: 14}
+        exclude:
+          - os: ubuntu-latest
+            toolchain: {compiler: gcc, version: 15}
+          - os: macos-latest
+            toolchain: {compiler: gcc, version: 14}
 
     steps:
-    - name: Set up Python 3.10
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - name: Checkout clawpack
-      uses: actions/[email protected]
+        python-version: ${{ matrix.python-version }}
+
+    - name: Set up compilers
+      uses: fortran-lang/setup-fortran@v1
+      id: setup-fortran
       with:
-        repository: clawpack/clawpack
+        compiler: ${{ matrix.toolchain.compiler }}
+        version: ${{ matrix.toolchain.version }}
+
     - name: Install dependencies
       run: |
-        sudo apt-get update
-        sudo apt-get install gfortran
-        # sudo apt-get liblapack-pic 
-        sudo apt-get install liblapack-dev
-        sudo apt-get install libnetcdf-dev libnetcdff-dev
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-    - name: Setup clawpack super repository
+        if [[ "${{ matrix.os }}" = "ubuntu-latest" ]]; then
+          sudo apt-get update
+          sudo apt-get install liblapack-dev
+          sudo apt-get install libnetcdf-dev libnetcdff-dev
+        elif [[ "${{ matrix.os }}" = "macos-latest" ]]; then
+          brew update
+          brew install netcdf netcdf-fortran
+        else
+          echo "${{ matrix.os }} not recognized."
+          exit 1
+        fi
+
+    - name: Install python dependencies
       run: |
-        git submodule init
-        git submodule update
-        pip install --user -e .
-    - name: Setup geoclaw
+        python -m pip install --upgrade pip
+        pip install flake8 meson-python ninja pytest numpy
+        pip install netCDF4 pandas xarray
+
+    - name: Checkout Clawpack
+      uses: actions/[email protected]
+      with:
+        repository: clawpack/clawpack
+        submodules: true
+
+    - name: Checkout GeoClaw branch
+      uses: actions/[email protected]
+      with:
+        path: geoclaw
+
+    - name: Install clawpack
       run: |
-        cd geoclaw
-        git checkout ${{ github.ref }}
+        cd ${CLAW}
+        pip install --no-build-isolation --editable .
+
     - name: Lint with flake8
       run: |
-        cd geoclaw
+        cd ${CLAW}/geoclaw
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude old_dtopotools.py
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
-        cd geoclaw
-        pytest
+        if [ "${{ matrix.toolchain.compiler }}" = "gcc" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-O0 -g -fcheck=all -fbacktrace -fbounds-check -ffpe-trap=invalid,zero,overflow -finit-real=nan -finit-integer=nan -Wall -Wunderflow -Wextra -Wconversion -Wuninitialized -Warray-bounds -Wshadow -Wno-unused-function -Wno-unused-variable -Wno-unused-parameter -Wno-unused-label -Wno-unused-but-set-variable"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="-O1 -fopenmp -funroll-loops -finline-functions -ftree-vectorize -fstack-protector-strong -flto -march=native"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel-classic" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip"
+            export OMP_NUM_THREADS=2
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "intel" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-O0 -debug all -check all -warn all,nodec,interfaces -gen_interfaces -traceback -fpe0 -ftrapuv -init=snan,arrays -check bounds"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="-O -qopenmp -unroll -finline-functions -inline-forceinline -ipo -ip"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "nvidia-hpc" ]; then
+          echo "nvidia-hpc compiler not yet supported"
+          exit 1
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS="-g -O0 -check all -traceback"
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="-O1 -qopenmp"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "flang" ]; then
+          echo "flang compiler not yet supported"
+          exit 1
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        elif [ "${{ matrix.toolchain.compiler }}" = "lfortran" ]; then
+          if [ "${{ matrix.build }}" = "debug" ]; then
+            export FFLAGS=""
+            export OMP_NUM_THREADS=1
+          elif [ "${{ matrix.build }}" = "opt" ]; then
+            export FFLAGS="--fast --openmp"
+            export OMP_NUM_THREADS=2
+          else
+            echo "Unknown build type: ${{ matrix.build }}"
+            exit 1
+          fi
+        else
+          echo "Unknown compiler: ${{ matrix.toolchain.compiler }}"
+          exit 1
+        fi
+        echo "FFLAGS: $FFLAGS"
+        echo "OMP_NUM_THREADS: $OMP_NUM_THREADS"
+        cd ${CLAW}/geoclaw
+        pytest --basetemp=./test_output
+
+    - name: Upload test results
+      if: failure()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test_results
+        path: ${{ env.CLAW }}/geoclaw/*_output
+        if-no-files-found: ignore

.gitignore

@@ -10,16 +10,22 @@ xamr
 xgeoclaw
 xgeoclaw.dSYM
 *.html
-_output/
-_plots/
+*_output/
+*_plots/
 *~
+# Topography
 *.asc
-*.tt3
-*.tt1
+*.tt*
+*.topotype*
 *.xyz
+
+# Scratch directory
 scratch/*
 !scratch/README.txt
+
+# Other data files
 *.nc
+
 # log files
 *.log
 

README.md

@@ -1,13 +1,16 @@
-# This repository hosts the GeoClaw code.
+# GeoClaw Package
+The GeoClaw version of Clawpack provides a specialized version of
+[Clawpack](https://www.clawpack.org) for various geophysical flow problems and 
+includes adaptive mesh refinement (AMR) based on 
+[AMRClaw](https://www.clawpack.org/amrclaw.html).
 
 See the main [clawpack/clawpack repository](https://github.com/clawpack/clawpack)
- README for more links.  
+README for more links.  
 
 See the [Documentation](https://www.clawpack.org/)
 for more details and installation instructions.
 
-
 **Links**
- - [Documentation for GeoClaw](https://www.clawpack.org/geoclaw.html)
- - [More description of GeoClaw and references](http://www.geoclaw.org)
- - [![Tests](https://github.com/clawpack/geoclaw/actions/workflows/testing.yml/badge.svg)](https://github.com/clawpack/geoclaw/actions/workflows/testing.yml)
+ - [Documentation](https://www.clawpack.org/geoclaw.html)
+ - [GeoClaw Web Site](https://www.geoclaw.org)
+ - ![Tests](https://github.com/clawpack/geoclaw/actions/workflows/testing.yml/badge.svg)

examples/1d_classic/shoaling_qinit_box/setplot.py

@@ -48,26 +48,26 @@ def add_annotations(current_data):
         title('')
         ylabel('meters', fontsize=14)
         if current_data.frameno == 0:
-            text(-95,-0.4,'$\longrightarrow$',fontsize=20)
+            text(-95,-0.4,r'$\longrightarrow$',fontsize=20)
             text(-95,-0.6,'Incident')
         h = current_data.q[0,:]
         mx2 = int(round(len(h)/2.))
         etamax2 = (h[:mx2] - hl).max()
         print('mx2 = %i, etamax2 = %g' % (mx2,etamax2))
         if (current_data.frameno == 5) and (etamax2 > 0.1):
-            text(-190,-0.5,'$\longleftarrow$',fontsize=20)
+            text(-190,-0.5,r'$\longleftarrow$',fontsize=20)
             text(-190,-0.7,'Reflected')
-            text(30,-0.5,'$\longrightarrow$',fontsize=20)
+            text(30,-0.5,r'$\longrightarrow$',fontsize=20)
             text(15,-0.7,'Transmitted')
         if (current_data.frameno == 6) and (etamax2 > 0.1):
-            text(-260,-0.5,'$\longleftarrow$',fontsize=20)
+            text(-260,-0.5,r'$\longleftarrow$',fontsize=20)
             text(-260,-0.7,'Reflected')
-            text(40,-0.5,'$\longrightarrow$',fontsize=20)
+            text(40,-0.5,r'$\longrightarrow$',fontsize=20)
             text(25,-0.7,'Transmitted')
         elif (current_data.frameno == 6):
-            text(-20,-0.5,'$\longleftarrow$',fontsize=20)
+            text(-20,-0.5,r'$\longleftarrow$',fontsize=20)
             text(-20,-0.7,'Reflected')
-            text(70,-0.5,'$\longrightarrow$',fontsize=20)
+            text(70,-0.5,r'$\longrightarrow$',fontsize=20)
             text(65,-0.7,'Transmitted')
 
 

examples/1d_classic/shoaling_qinit_step/make_plots_for_paper.py

@@ -49,7 +49,7 @@ def save_figure(fname):
     plot(xgrid,0*zgrid,'b')
     ylim(-3500,300)
 #title('Bathymetry')
-xticks([-xs,0,xs],['$-\epsilon$','0','$\epsilon$'])
+xticks([-xs,0,xs],[r'$-\epsilon$','0',r'$\epsilon$'])
 xlim(xlimits)
 ylabel('meters')
 
@@ -71,8 +71,8 @@ def save_figure(fname):
     if t==0:
         title('t = 0')
     else:
-        title('t = %4.3f$ \epsilon$' % txs)
-    xticks([-xs,0,xs],['$-\epsilon$','0','$\epsilon$'])
+        title(r't = %4.3f$ \epsilon$' % txs)
+    xticks([-xs,0,xs],[r'$-\epsilon$','0',r'$\epsilon$'])
 
     hl = 3200.
     hr = 200.

examples/1d_classic/shoaling_qinit_step/setplot.py

@@ -47,7 +47,7 @@ def add_annotation(current_data):
         ylabel('meters', fontsize=14)
 
         if current_data.frameno == 0:
-            text(-80,-0.4,'$\longrightarrow$',fontsize=20)
+            text(-80,-0.4,r'$\longrightarrow$',fontsize=20)
             text(-80,-0.6,'Incident')
         h = current_data.q[0,:]
         mx2 = int(round(len(h)/2.))

examples/bowl-slosh-netcdf/.gitignore

@@ -0,0 +1,2 @@
+bowl.nc
+netcdf_test

examples/tsunami/bowl-slosh-netcdf/Makefile → examples/bowl-slosh-netcdf/Makefile

@@ -22,8 +22,8 @@ PLOTDIR = _plots               # Directory for plots
 # Environment variable FC should be set to fortran compiler, e.g. gfortran
 
 # Compiler flags can be specified here or set as an environment variable
-FFLAGS += -DNETCDF -lnetcdf -I$(NETCDF4_DIR)/include -L$(NETCDF4_DIR)/lib
-LFLAGS += $(FFLAGS) -lnetcdff
+FFLAGS += -DNETCDF -I$(NETCDF4_DIR)/include -L$(NETCDF4_DIR)/lib
+LFLAGS += -I$(NETCDF4_DIR)/include -L$(NETCDF4_DIR)/lib -lnetcdff
 
 
 # ---------------------------------
@@ -60,7 +60,7 @@ SOURCES = \
 include $(CLAWMAKE)
 
 # Construct the topography data
-.PHONY: topo all
+.PHONY: topo all netcdf_test netcdf_clean netcdf_clobber
 topo:
 	$(CLAW_PYTHON) maketopo.py
 
@@ -69,3 +69,18 @@ all:
 	$(MAKE) .plots
 	$(MAKE) .htmls
 
+netcdf_test: netcdf_test.f90
+	$(FC) netcdf_test.f90 $(FFLAGS) $(LFLAGS) -o netcdf_test
+
+netcdf_clobber:
+	-rm -f  netcdf_test.o 
+
+netcdf_clean:
+	-rm -f netcdf_test
+
+# Requires :: syntax in Makefile.common to work
+# clobber::
+# 	-rm -f  netcdf_test.o 
+
+# clean::
+# 	-rm -f netcdf_test