debugging codecov build #4

Workflow file for this run

.github/workflows/coverage.yml at 939ab29

	# Code Coverage workflow
	# Builds MPAS with coverage instrumentation, runs test cases, and uploads to Codecov
	#
	# Note: GCC coverage requires .gcno files (compile-time) and .gcda files (runtime)
	# to be in matching locations. We handle this by:
	# 1. Building in a known location
	# 2. Using GCOV_PREFIX/GCOV_PREFIX_STRIP to redirect .gcda output
	# 3. Processing coverage in the same container for gcov compatibility
	#
	name: Code Coverage

	on:
	workflow_dispatch:
	inputs:
	test-case:
	description: 'Test case to run'
	type: choice
	default: '240km'
	options:
	- 240km
	push:
	branches:
	- master
	- feature-ci
	pull_request:
	branches:
	- master
	- feature-ci

	jobs:
	#===========================================================================
	# BUILD, RUN, AND GENERATE COVERAGE in single job
	# This avoids path mismatches between compile and runtime
	#===========================================================================
	coverage:
	name: Build, Run, and Generate Coverage
	runs-on: ubuntu-latest
	container:
	image: ncarcisl/cisldev-x86_64-almalinux9-gcc-mpich3:devel

	steps:
	- uses: actions/checkout@v4
	with:
	submodules: 'true'

	- name: Install coverage tools
	run: \|
	# Install lcov for coverage report generation
	# lcov is in EPEL for AlmaLinux/RHEL 9
	echo "Installing EPEL repository..."
	dnf install -y epel-release

	echo "Installing lcov..."
	dnf install -y lcov

	lcov --version

	- name: Build MPAS-A with coverage flags
	run: \|
	# Source container environment
	if [ -f /container/config_env.sh ]; then
	source /container/config_env.sh
	fi

	# Patch Makefile to add coverage flags to the gfortran target
	# This preserves the proper dependency handling for parallel builds
	echo "Patching Makefile for coverage instrumentation..."

	# Add --coverage to FFLAGS_OPT in gfortran target
	sed -i 's/"FFLAGS_OPT = -O3 -ffree-line-length-none/"FFLAGS_OPT = -O0 --coverage -g -ffree-line-length-none/' Makefile

	# Add --coverage to CFLAGS_OPT in gfortran target
	sed -i 's/"CFLAGS_OPT = -O3"/"CFLAGS_OPT = -O0 --coverage -g"/' Makefile

	# Add --coverage to CXXFLAGS_OPT in gfortran target
	sed -i 's/"CXXFLAGS_OPT = -O3"/"CXXFLAGS_OPT = -O0 --coverage -g"/' Makefile

	# Add --coverage to LDFLAGS_OPT in gfortran target
	sed -i 's/"LDFLAGS_OPT = -O3"/"LDFLAGS_OPT = --coverage"/' Makefile

	# Verify the patch worked
	echo "=== Patched FFLAGS_OPT ==="
	grep "FFLAGS_OPT.*coverage" Makefile \| head -1

	# Build with parallel jobs (dependency order handled by gfortran target)
	make gfortran CORE=atmosphere --jobs $(nproc)

	# Verify gcno files were created
	echo "=== .gcno files created ==="
	find src -name "*.gcno" \| wc -l
	find src -name "*.gcno" \| head -10

	- name: Run 240km test case
	run: \|
	# Source container environment
	if [ -f /container/config_env.sh ]; then
	source /container/config_env.sh
	fi

	# Extract test case
	tar xzf .github/workflows/240km.tar.gz
	cd 240km

	# Link executable
	ln -sf ../atmosphere_model .

	# Configure for a short run
	sed -i "s/config_run_duration = '[^']*'/config_run_duration = '0_00:30:00'/" namelist.atmosphere

	# Run model - gcda files will be generated in src/ directory
	# because that's where the gcno files are
	ulimit -s unlimited 2>/dev/null \|\| true
	mpirun -n 1 ./atmosphere_model \|\| {
	echo "Model run completed (may have warnings)"
	}

	cd ..

	# Verify gcda files were created
	echo "=== .gcda files created ==="
	find . -name "*.gcda" \| wc -l
	find . -name "*.gcda" \| head -10

	- name: Generate coverage report
	run: \|
	# Source container environment for gcov
	if [ -f /container/config_env.sh ]; then
	source /container/config_env.sh
	fi

	# Debug: Show what we have
	echo "=== Coverage files summary ==="
	echo "gcno files: $(find . -name '*.gcno' \| wc -l)"
	echo "gcda files: $(find . -name '*.gcda' \| wc -l)"

	# Check if we have both gcno and gcda files
	if [ $(find . -name '*.gcda' \| wc -l) -eq 0 ]; then
	echo "WARNING: No .gcda files found - model may not have run correctly"
	echo "Listing directory structure for debugging:"
	ls -la
	ls -la 240km/ \|\| true
	fi

	# Generate lcov report
	# Use gcov from the container (matches compiler version)
	lcov --capture \
	--directory src \
	--output-file coverage.info \
	--ignore-errors source,gcov,empty \
	\|\| echo "Warning: lcov had some errors (this may be okay)"

	# Check if coverage.info has content
	if [ -s coverage.info ]; then
	# Remove external/system files from coverage
	lcov --remove coverage.info \
	'/usr/*' \
	'/external/' \
	--output-file coverage.info \
	--ignore-errors unused \
	\|\| true

	# Generate summary
	echo "=== Coverage Summary ==="
	lcov --list coverage.info \|\| true
	else
	echo "WARNING: coverage.info is empty or missing"
	# Create minimal coverage file for debugging
	echo "TN:" > coverage.info
	echo "SF:src/placeholder.F" >> coverage.info
	echo "end_of_record" >> coverage.info
	fi

	- name: Upload to Codecov
	uses: codecov/codecov-action@v4
	with:
	files: coverage.info
	flags: fortran
	name: mpas-atmosphere
	fail_ci_if_error: false
	verbose: true
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

	- name: Upload coverage artifacts
	uses: actions/upload-artifact@v4
	if: always()
	with:
	name: coverage-report
	path: \|
	coverage.info
	retention-days: 30

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debugging codecov build #4

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debugging codecov build #4

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