Merge branch 'development' into derive_rates

.clang-tidy

@@ -19,6 +19,7 @@ Checks: >
        -misc-include-cleaner,
        -misc-non-private-member-variables-in-classes,
        -misc-use-anonymous-namespace,
+       -misc-use-internal-linkage,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
@@ -29,12 +30,14 @@ Checks: >
        -readability-avoid-const-params-in-decls,
        -readability-braces-around-statements,
        -readability-else-after-return,
+       -readability-enum-initial-value,
        -readability-function-cognitive-complexity,
        -readability-function-size,
        -readability-identifier-length,
        -readability-implicit-bool-conversion,
        -readability-isolate-declaration,
        -readability-magic-numbers,
+       -readability-math-missing-parentheses,
        -readability-named-parameter,
        -readability-simplify-boolean-expr,
      mpi-*,

.github/workflows/burn_cell_metal_chem.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Compile
         run: |
           cd unit_test/burn_cell_metal_chem
-          make -j 2
+          make -j 4
 
       - name: Run and compare outputs for different Z values, also including cosmic ray ionization
         run: |

.github/workflows/burn_cell_primordial_chem.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Compile and run
         run: |
           cd unit_test/burn_cell_primordial_chem
-          make -j 2
+          make -j 4
           ./main1d.gnu.DEBUG.ex inputs_primordial_chem amrex.fpe_trap_{invalid,zero,overflow}=1 > test.out
 
       - name: Print backtrace

.github/workflows/c-linter.yml

@@ -26,7 +26,7 @@ jobs:
         uses: AMReX-Astro/cpp-linter-action@main
         with:
           build_path: 'unit_test/test_react'
-          make_options: '-j 2 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
+          make_options: '-j 4 USE_OMP=FALSE USE_MPI=FALSE USE_CUDA=FALSE DEBUG=TRUE'
           ignore_files: 'amrex|util/gcem'
           header_filter: '(/conductivity/|/constants/|/EOS/|/integration/|/interfaces/|/networks/|/neutrinos/|/nse_solver/|/opacity/|/rates/|/screening/|/util/|^\./).*\.H$'
           config_file: ${GITHUB_WORKSPACE}/.clang-tidy

.github/workflows/castro-development.yml

@@ -47,7 +47,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/flame_wave/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
@@ -64,7 +64,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/subchandra/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache

.github/workflows/castro.yml

@@ -51,7 +51,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/flame_wave/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache
@@ -68,7 +68,7 @@ jobs:
         export MICROPHYSICS_HOME=${PWD}
 
         cd Castro/Exec/science/subchandra/
-        make -j2 CCACHE=ccache USE_MPI=FALSE
+        make -j 4 CCACHE=ccache USE_MPI=FALSE
 
         ccache -s
         du -hs ~/.cache/ccache

.github/workflows/clang-tidy.yml

@@ -26,10 +26,10 @@ jobs:
 
       - name: Install dependencies
         run: |
-          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 19
 
       - name: Compile burn_cell_sdc
         run: |
           cd unit_test/burn_cell_sdc
-          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-19 CLANG_TIDY_WARN_ERROR=TRUE -j 4
 

.github/workflows/cmake_build_cell_primordial_chem.yml

@@ -18,5 +18,5 @@ jobs:
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure

.github/workflows/cuda.yml

@@ -26,23 +26,23 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies/dependencies_nvcc11.sh
+        run: .github/workflows/dependencies/dependencies_nvcc.sh 11.7
 
       - name: compile test_react (aprox13)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_react
-          make NETWORK_DIR=aprox13 USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make NETWORK_DIR=aprox13 USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
 
       - name: compile test_react (ignition_reaclib/URCA-simple)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_react
           make realclean
-          make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4
 
       - name: compile test_nse_net (ase)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_nse_net
-          make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 4

.github/workflows/dependencies/dependencies_hip.sh

@@ -40,6 +40,7 @@ echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/r
 
 # we should not need to export HIP_PATH=/opt/rocm/hip with those installs
 
+sudo apt-get clean
 sudo apt-get update
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#installing-development-packages-for-cross-compilation
@@ -56,7 +57,9 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev
+    rocfft-dev      \
+    rocprim-dev     \
+    rocsparse-dev
 
 # hiprand-dev is a new package that does not exist in old versions
 sudo apt-get install -y --no-install-recommends hiprand-dev || true

.github/workflows/dependencies/dependencies_nvcc.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020-2022 Axel Huebl
+#
+# License: BSD-3-Clause-LBNL
+
+set -eu -o pipefail
+
+# `man apt.conf`:
+#   Number of retries to perform. If this is non-zero APT will retry
+#   failed files the given number of times.
+echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
+sudo apt-get -qqq update
+sudo apt-get install -y \
+    build-essential     \
+    ca-certificates     \
+    cmake               \
+    g++                 \
+    gfortran            \
+    gnupg               \
+    libopenmpi-dev      \
+    openmpi-bin         \
+    pkg-config          \
+    wget
+
+VERSION_DOTTED=${1-12.0} && VERSION_DASHED=$(sed 's/\./-/' <<< $VERSION_DOTTED)
+curl -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
+sudo dpkg -i cuda-keyring_1.0-1_all.deb
+sudo apt-get update
+sudo apt-get install -y \
+    cuda-command-line-tools-$VERSION_DASHED \
+    cuda-compiler-$VERSION_DASHED           \
+    cuda-cupti-dev-$VERSION_DASHED          \
+    cuda-minimal-build-$VERSION_DASHED      \
+    cuda-nvml-dev-$VERSION_DASHED           \
+    cuda-nvtx-$VERSION_DASHED               \
+    libcufft-dev-$VERSION_DASHED            \
+    libcurand-dev-$VERSION_DASHED           \
+    libcusparse-dev-$VERSION_DASHED
+sudo ln -s cuda-$VERSION_DOTTED /usr/local/cuda

.github/workflows/docs-test.yml

@@ -35,10 +35,10 @@ jobs:
 
       - name: Build docs
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS='-v -W --keep-going' html
 
       - name: Link check
         run: |
-          cd sphinx_docs/
+          cd Docs/
           make SPHINXOPTS=-v linkcheck

.github/workflows/macos_build_cell_metal_chem.yml

@@ -12,11 +12,10 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite [email protected]
 
       - name: Compile and run
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_MC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure

.github/workflows/macos_build_cell_primordial_chem.yml

@@ -12,11 +12,10 @@ jobs:
       - name: Install dependencies
         run: |
           brew install cmake openmpi python3 || true
-          brew link --overwrite [email protected]
 
       - name: Compile and run
         run: |
           mkdir build && cd build
           cmake .. -DBUILD_UNIT_TEST_PC=true -DBUILD_AMReX=true
-          make -j2
+          make -j 4
           ctest --output-on-failure

.github/workflows/test_neutrinos.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Compile
         run: |

.github/workflows/test_partition_functions.yml

@@ -0,0 +1,44 @@
+name: test_partition_functions
+
+on: [pull_request]
+jobs:
+  test_partition_functions:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile
+        run: |
+          cd unit_test/test_part_func
+          make clean
+          make -j 4
+
+      - name: Run test_part_func
+        run: |
+          cd unit_test/test_part_func
+          ./main3d.gnu.ex > test.out
+
+      - name: Compare to stored output
+        run: |
+          cd unit_test/test_part_func
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/part_func.out
+

.github/workflows/test_rhs.yml

@@ -29,7 +29,7 @@ jobs:
       - name: Build the fextrema tool
         run: |
           cd external/amrex/Tools/Plotfile
-          make programs=fextrema -j 2
+          make programs=fextrema -j 4
 
       - name: Compile, test_rhs (VODE, ignition_simple)
         run: |

.gitignore

@@ -78,7 +78,7 @@ extern.f90
 # sphinx
 build/
 doxy_files
-sphinx_docs/source/runtime_parameters.rst
+Docs/source/runtime_parameters.rst
 
 
 # C++ parameters

CHANGES.md

@@ -1,3 +1,23 @@
+# 25.01
+
+  * update HIP/CUDA dependences to include sparse libraries (#1686)
+
+  * rename `Opacity_dir` -> `OPACITY_DIR` (#1679)
+
+  * update the integration and NSE docs (#1682)
+
+# 24.12
+
+  * documentation improvements (#1661, #1667, #1670)
+
+  * optimize tabular NSE EOS calls (#1668)
+
+  * CI fixes (#1666, #1671, #1675) and new partition function CI
+    (#1673)
+
+  * `burn_cell` can now initialize all mass fractions to be equal
+    (#1665)
+
 # 24.10
 
   * metal chemistry updates (#1648) with ices (#1650) and cosmic rays (#1651)

sphinx_docs/source/conf.py → Docs/source/conf.py

@@ -223,8 +223,11 @@ def get_version():
 
 linkcheck_retries = 3
 linkcheck_timeout = 100
+linkcheck_allow_unauthorized = True
+linkcheck_ignore = [r"https://doi.org/10.1103/[Pp]hys[Rr]ev*"]
 user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"
 
+
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples