Trees issues fixes

.ci/check_hdf5_docs.sh

@@ -0,0 +1,18 @@
+# Generate the HDF5 output documentation and check it's up to date
+# otherwise tell the user how to update it
+hdf5_file="$1"
+rst_file="$2"
+hdf5_file_basename=`basename "${hdf5_file}"`
+full_rst_file="doc/hdf5_properties/${rst_file}"
+
+scripts/properties_as_list.sh "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${hdf5_file}" > props.rst
+_diff="`diff -Naur "${full_rst_file}" props.rst`"
+if [ -n "${_diff}" ]; then
+	echo "\nThe file ${full_rst_file} is out of date. This probably means that you added a new\n" \
+	"dataset to shark's output, but forgot to update the corresponding documentation.\n" \
+	"The full difference follows:\n\n${_diff}\n\n" \
+	"Please run the script/properties_as_lish.sh script against a ${hdf5_file_basename} file\n" \
+	"to re-generate its documentation, then commit your changes. For example:\n\n" \
+	"scripts/properties_as_list.sh my-output/model/199/0/${hdf5_file_basename} > ${full_rst_file}" >&2
+	exit 1
+fi

.ci/compare_galaxies.sh

@@ -0,0 +1,9 @@
+reference_model_name=$1
+shift
+this_model_name=$1
+shift
+
+python scripts/compare_galaxies.py -m \
+  "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${reference_model_name}/199/0/galaxies.hdf5" \
+  "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${this_model_name}/199/0/galaxies.hdf5" \
+  $@

.ci/run_shark.sh

@@ -0,0 +1,10 @@
+model_name=$1
+shift
+
+${CI_BUILD_DIR}/shark ${TEST_CONFIG_FILE} \
+    -o execution.output_bh_histories=true -o execution.snapshots_bh_histories=199 \
+    -o simulation.redshift_file=${TEST_INPUTS_DIR}/redshifts.txt \
+    -o simulation.tree_files_prefix=${TEST_INPUTS_DIR}/tree_199 \
+    -o simulation.sim_name=${TEST_SIM_NAME} \
+    -o execution.name_model=$model_name \
+    $@

.github/actions/download-shark-build/action.yaml

@@ -0,0 +1,17 @@
+name: Get shark up and running from previous build
+runs:
+  using: composite
+  steps:
+    - name: Download shark build tarball
+      uses: actions/download-artifact@v3
+      with:
+        name: shark-build
+
+    - name: Untar shark build after download
+      run: tar xf shark-build.tar.gz
+      shell: bash
+
+    - name: Install system runtime dependencies
+      run: sudo apt install libhdf5-103 libboost-filesystem1.74.0 libboost-program-options1.74.0 libboost-log1.74.0 libgsl27
+      shell: bash
+

.github/actions/setup-config-file/action.yaml

@@ -0,0 +1,12 @@
+name: Setup the shark configuration file used for tests
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        sed "
+          s|output_directory.*|output_directory = ${TEST_OUTPUTS_DIR}|
+          s|redshift_file.*|redshift_file = ${TEST_INPUTS_DIR}/redshifts.txt|
+          s|tree_files_prefix.*|tree_files_prefix = ${TEST_INPUTS_DIR}/tree_199|
+          s|sim_name.*|sim_name = ${TEST_SIM_NAME}|
+        " sample.cfg > ${{ env.TEST_CONFIG_FILE }}
+      shell: bash

.github/workflows/build-and-test.yaml

@@ -1,40 +1,196 @@
 name: Build and test
+on: [push, pull_request]
 
-# Build on every branch push, tag push, and pull request change:
-on: [push]
+env:
+  CI_BUILD_DIR: build
+  TEST_INPUTS_DIR: inputs
+  TEST_OUTPUTS_DIR: outputs
+  TEST_CONFIG_FILE: ci-tests.cfg
+  TEST_SIM_NAME: mini-SURFS
+  TEST_FIXED_SEED: 123456
 
 jobs:
-  build_wheels:
-    name: Build and test shark on ${{ matrix.os }}
+  build_and_test:
+    name: Build and test shark. OS=${{ matrix.os }}, omp=${{ matrix.omp }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        #os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
+        omp: [true, false]
 
     steps:
       - uses: actions/checkout@v3
         with:
           submodules: true
 
-      - name: Install dependencies
+      - name: Install system dependencies (Linux)
         if: ${{ matrix.os == 'ubuntu-latest' }}
         run: |
-          sudo apt install libhdf5-dev hdf5-tools libboost-filesystem-dev libboost-program-options-dev libboost-log-dev cxxtest libgsl-dev
+          sudo apt install ninja-build libhdf5-dev hdf5-tools libboost-filesystem-dev libboost-program-options-dev libboost-log-dev cxxtest libgsl-dev
 
-      - name: Install dependencies
+      - name: Install system dependencies (MacOS)
         if: ${{ matrix.os == 'macos-latest' }}
         run: |
-          brew install hdf5 boost cxxtest gsl
+          brew install ninja hdf5 boost cxxtest gsl ${{ matrix.omp && 'libomp' || '' }}
+
+      - name: Point CMake to libomp (MacOS)
+        if: ${{ matrix.os == 'macos-latest' && matrix.omp }}
+        run: |
+          # libomp is installed as keg-only, so we need to manually point to it
+          HOMEBREW_LIBOMP_PREFIX=`brew --prefix libomp`
+          OMP_FLAGS="-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include"
+          echo "EXTRA_CMAKE_ARGS=-DOpenMP_C_FLAGS=\"$OMP_FLAGS\" -DOpenMP_C_LIB_NAMES=omp -DOpenMP_CXX_FLAGS=\"$OMP_FLAGS\" -DOpenMP_CXX_LIB_NAMES=omp -DOpenMP_omp_LIBRARY=$HOMEBREW_LIBOMP_PREFIX/lib/libomp.dylib" >> "$GITHUB_ENV"
 
       - name: Configure
-        # Leaving Werror out for now because there *are* errors
-        # and I don't know what the proper fix is.
-        run: cmake -B build/ -DSHARK_TEST=ON -DCMAKE_CXX_FLAGS="-Wall" #-Werror
+        run: |
+          eval cmake -B ${CI_BUILD_DIR} -G Ninja \
+            -DSHARK_TEST=ON -DSHARK_NO_OPENMP=${{ matrix.omp && 'OFF' || 'ON' }} -DCMAKE_CXX_FLAGS="-Wall -Werror" \
+            $EXTRA_CMAKE_ARGS
 
       - name: Build
-        run: cmake --build build/
+        run: cmake --build ${CI_BUILD_DIR}
 
       - name: Run unit tests
         run: |
-          cd build
+          cd ${CI_BUILD_DIR}
           ctest --output-on-failure
+
+      - name: Tar shark build before upload
+        run: tar cf shark-build.tar.gz ${{ env.CI_BUILD_DIR }}
+
+      - name: Upload shark build for next jobs (Linux)
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.omp }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: shark-build
+          path: shark-build.tar.gz
+
+  initial_shark_run:
+    name: Initial shark run (with fixed seed)
+    needs: build_and_test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: ./.github/actions/download-shark-build
+
+      - name: Download test datasets
+        run: |
+          mkdir -p ${TEST_INPUTS_DIR}
+          curl -L -o ${TEST_INPUTS_DIR}/redshifts.txt 'https://docs.google.com/uc?export=download&id=1xvNmJB_KmoBHuQz-QzdPnY0HFs7smkUB'
+          curl -L -o ${TEST_INPUTS_DIR}/tree_199.0.hdf5 'https://docs.google.com/uc?export=download&id=1JDK8ak13bEhzg9H9xt0uE8Fh_2LD3KpZ'
+
+      - uses: ./.github/actions/setup-config-file
+
+      - name: Run shark with fixed seed
+        run: .ci/run_shark.sh my_model -o execution.seed=${TEST_FIXED_SEED}
+
+      - name: Upload shark output for next jobs
+        uses: actions/upload-artifact@v3
+        with:
+          name: shark-output
+          path: ${{ env.TEST_OUTPUTS_DIR }}
+
+      - name: Upload shark inputs for next jobs
+        uses: actions/upload-artifact@v3
+        with:
+          name: shark-input
+          path: ${{ env.TEST_INPUTS_DIR }}
+
+  check_hdf5_docs:
+    name: Check HDF5 properties documentation is up to date
+    needs: initial_shark_run
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install HDF5 tools
+        run: sudo apt install hdf5-tools
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: shark-output
+          path: ${{ env.TEST_OUTPUTS_DIR }}
+
+      - name: Check output properties' documentation
+        run: |
+          .ci/check_hdf5_docs.sh my_model/199/0/galaxies.hdf5 galaxies.rst
+          .ci/check_hdf5_docs.sh my_model/156/0/star_formation_histories.hdf5 star_formation_histories.rst
+          .ci/check_hdf5_docs.sh my_model/199/0/black_hole_histories.hdf5 black_hole_histories.rst
+
+  generate_plots:
+    name: Generate all standard plots
+    needs: initial_shark_run
+    runs-on: ubuntu-latest
+    # Currently skipped because there are a few minor problems
+    # with some plots
+    if: false
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: shark-output
+          path: ${{ env.TEST_OUTPUTS_DIR }}
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Python dependencies
+        run: pip install matplotlib h5py scipy
+
+      - uses: ./.github/actions/setup-config-file
+
+      - name: Generate all plots
+        run: |
+          echo "backend: Agg" >> matplotlibrc
+          python standard_plots/all.py -c ${{ env.TEST_CONFIG_FILE }}
+
+  check_reproducibility:
+    name: Check shark runs are reproducible
+    needs: initial_shark_run
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: ./.github/actions/download-shark-build
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: shark-output
+          path: ${{ env.TEST_OUTPUTS_DIR }}
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: shark-input
+          path: ${{ env.TEST_INPUTS_DIR }}
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Python dependencies
+        run: pip install h5py
+
+      - uses: ./.github/actions/setup-config-file
+
+      - name: Check fixed seed is reproducible
+        run: |
+          .ci/run_shark.sh my_model_same_seed -o execution.seed=${TEST_FIXED_SEED}
+          .ci/compare_galaxies.sh my_model my_model_same_seed
+
+      - name: Check fixed seed is reproducible when multithreaded
+        run: |
+          # "-t 0" lets shark use the maximum number of OpenMP threads,
+          # which OpenMP implementations usually constrain to the available hardware
+          .ci/run_shark.sh my_model_same_seed_parallel -o execution.seed=123456 -t 0
+          .ci/compare_galaxies.sh my_model my_model_same_seed_parallel
+
+      - name: Check random seed gives different results
+        run: |
+          .ci/run_shark.sh my_model_random_seed -t 0
+          .ci/compare_galaxies.sh my_model my_model_random_seed --expect-unequal

.github/workflows/build-docs.yml

@@ -0,0 +1,15 @@
+name: Build documentation
+on: [push, pull_request]
+env:
+  SPHINXOPTS: -W --keep going
+
+jobs:
+  build-docs:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "doc"
+        pre-build-command: 'pip install -U sphinx_rtd_theme docutils'

.readthedocs.yaml

@@ -1,4 +1,8 @@
 version: 2
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
 
 submodules:
   include: all

.travis/test.sh

@@ -43,6 +43,7 @@ curl -L -o input/tree_199.0.hdf5 'https://docs.google.com/uc?export=download&id=
 run_shark() {
 	model_name=$1; shift
 	./shark ../sample.cfg \
+	    -o execution.output_bh_histories=true -o execution.snapshots_bh_histories=199 \
 	    -o simulation.redshift_file=input/redshifts.txt \
 	    -o simulation.tree_files_prefix=input/tree_199 \
 	    -o execution.name_model=$model_name $@ || fail "failure during execution of shark"
@@ -67,6 +68,7 @@ check_hdf5_doc() {
 
 check_hdf5_doc 199/0/galaxies.hdf5 galaxies.rst
 check_hdf5_doc 156/0/star_formation_histories.hdf5 star_formation_histories.rst
+check_hdf5_doc 199/0/black_hole_histories.hdf5 black_hole_histories.rst
 
 if [ -n "$PYTHON" ]; then
 

CMakeLists.txt

@@ -175,7 +175,7 @@ macro(find_boost)
 	# with homebrew). Let's thus not use Boost's cmake config file and stick to
 	# cmake's own version of it for the time being
 	set(Boost_NO_BOOST_CMAKE ON)
-	find_package(Boost 1.54 COMPONENTS filesystem log program_options system REQUIRED)
+	find_package(Boost 1.68 COMPONENTS filesystem log program_options system REQUIRED)
 	set(SHARK_LIBS ${SHARK_LIBS} ${Boost_LIBRARIES})
 	include_directories(${Boost_INCLUDE_DIRS})
 endmacro()
@@ -185,7 +185,7 @@ endmacro()
 #
 macro(find_openmp)
 	find_package(OpenMP)
-	if (OPENMP_FOUND)
+	if (OpenMP_FOUND)
 
 		# We require at least OpenMP 2.0, so let's double check
 		# we have that at least
@@ -196,9 +196,11 @@ macro(find_openmp)
 		#   and OpenMP_<lang>_LIBRARIES/LIBRARY/LIB_NAMES variables
 		# This is important for Intel compilers in particular, which require
 		# additional linking
-		if ((DECLARED OPENMP_VERSION) AND (NOT OPENMP_VERSION VERSION_LESS 2.0))
+		if ((DEFINED OpenMP_VERSION) AND (NOT OpenMP_VERSION VERSION_LESS 2.0))
 			set(SHARK_OPENMP ON)
-		elseif((DECLARED OPENMP_CXX_SPEC_DATE) AND (NOT OPENMP_CXX_SPEC_DATE LESS 200203))
+		elseif ((DEFINED OpenMP_CXX_VERSION) AND (NOT OpenMP_CXX_VERSION VERSION_LESS 2.0))
+			set(SHARK_OPENMP ON)
+		elseif ((DEFINED OpenMP_CXX_SPEC_DATE) AND (NOT OpenMP_CXX_SPEC_DATE LESS 200203))
 			set(SHARK_OPENMP ON)
 		else()
 			set(OPENMP_VERSION_CHECK_SOURCE "
@@ -237,9 +239,10 @@ int main(int argc, char *argv[]) {
 	endif()
 
 	if (SHARK_OPENMP)
-		add_compile_options("${OpenMP_CXX_FLAGS}")
+		string(REPLACE " " ";" OpenMP_CXX_FLAGS_as_list ${OpenMP_CXX_FLAGS})
+		add_compile_options(${OpenMP_CXX_FLAGS_as_list})
 		set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
-		set(SHARK_LIBS ${SHARK_LIBS} ${OpenMP_CXX_LIBRARIES})
+		list(APPEND SHARK_LIBS ${OpenMP_CXX_LIBRARIES})
 	endif()
 endmacro()
 

doc/building.rst

@@ -19,7 +19,7 @@ Requirements
 
 * `GSL <https://www.gnu.org/software/gsl/>`_ >= 2.0
 * `HDF5 <https://support.hdfgroup.org/HDF5/>`_ >= 1.8.0
-* `Boost <http://www.boost.org/>`_ >= 1.54
+* `Boost <http://www.boost.org/>`_ >= 1.68
 
 Optional requirements are: