Merge branch 'AMReX-Astro:main' into current_inputs

.clang-tidy

@@ -7,23 +7,23 @@ Checks: >
      clang-diagnostic-*,
      cppcoreguidelines-*,
        -cppcoreguidelines-avoid-c-arrays,
+       -cppcoreguidelines-avoid-do-while,
        -cppcoreguidelines-avoid-magic-numbers,
        -cppcoreguidelines-avoid-non-const-global-variables,
        -cppcoreguidelines-init-variables,
        -cppcoreguidelines-interfaces-global-init,
        -cppcoreguidelines-macro-usage,
-       -cppcoreguidelines-no-malloc,
        -cppcoreguidelines-non-private-member-variables-in-classes,
        -cppcoreguidelines-owning-memory,
        -cppcoreguidelines-pro-*,
      misc-*,
        -misc-const-correctness,
        -misc-include-cleaner,
        -misc-non-private-member-variables-in-classes,
+       -misc-no-recursion,
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
-       -modernize-use-using,
      performance-*,
        -performance-avoid-endl,
      portability-*,

.github/workflows/c-linter.yml

@@ -2,6 +2,10 @@ name: cpp-linter
 
 on: [pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   cpp-linter:
     runs-on: ubuntu-latest

.github/workflows/check_pr_branch.yml

@@ -0,0 +1,20 @@
+name: check PR branch
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - edited
+
+jobs:
+  check-PR-branch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: PRs should not target main
+        run: |
+          if [[ "${{ github.base_ref }}" == "main" ]]; then
+            echo 'Pull requests must not be made against main. Please target development instead.'
+            exit 1
+          fi

.github/workflows/clang-tidy.yml

@@ -0,0 +1,36 @@
+name: "clang-tidy"
+
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  clang_tidy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          echo "MICROPHYSICS_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../amrex
+          git fetch; git checkout development
+          echo "AMREX_HOME=$(pwd)" >> $GITHUB_ENV
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          .github/workflows/dependencies_clang-tidy-apt-llvm.sh 17
+
+      - name: Compile flame_wave
+        run: |
+          echo $AMREX_HOME
+          echo $MICROPHYSICS_HOME
+          cd Exec/science/subchandra
+          make USE_MPI=FALSE USE_CLANG_TIDY=TRUE CLANG_TIDY=clang-tidy-17 CLANG_TIDY_WARN_ERROR=TRUE -j 4
+

.github/workflows/compiler-warnings.yml

@@ -1,6 +1,11 @@
 name: "compiler warnings"
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   compiler_warnings:
     runs-on: ubuntu-latest

.github/workflows/dependencies_clang-tidy-apt-llvm.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+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
+
+if [[ ! -f /etc/apt/trusted.gpg.d/apt.llvm.org.asc ]]; then
+    wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
+fi
+
+source /etc/os-release # set UBUNTU_CODENAME
+
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME} main"
+sudo add-apt-repository "deb http://apt.llvm.org/${UBUNTU_CODENAME}/ llvm-toolchain-${UBUNTU_CODENAME}-$1 main"
+
+sudo apt-get update
+
+sudo apt-get install -y --no-install-recommends \
+    clang-tidy-$1 libomp-$1-dev

.github/workflows/detonation-sdc-compare.yml

@@ -1,6 +1,11 @@
 name: detonation-sdc
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   detonation-sdc:
     runs-on: ubuntu-latest

.github/workflows/flame_wave-compare.yml

@@ -1,6 +1,11 @@
 name: flame_wave
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   flame_wave-2d:
     runs-on: ubuntu-latest
@@ -31,7 +36,7 @@ jobs:
       - name: Run flame_wave
         run: |
           cd Exec/science/flame_wave
-          ./Castro2d.gnu.DEBUG.ex inputs_2d.testsuite max_step=2 castro.sum_interval=1 amr.plot_files_output=0 amr.checkpoint_files_output=0
+          ./Castro2d.gnu.DEBUG.ex inputs_2d.testsuite max_step=2 castro.sum_interval=1 amr.plot_files_output=1 amr.checkpoint_files_output=0
 
       - name: Check grid_diag.out
         run: |
@@ -42,3 +47,10 @@ jobs:
         run: |
           cd Exec/science/flame_wave
           diff species_diag.out ci-benchmarks/species_diag.out
+
+      - name: Check job_info parameters
+        run: |
+          cd Exec/science/flame_wave
+          line_no=`grep -n "Inputs File Parameters" plt00000/job_info | cut -d ":" -f 1`
+          tail -n +$(($line_no -1)) plt00000/job_info > tmp.txt
+          diff tmp.txt ci-benchmarks/job_info_params.txt

.github/workflows/fsanitizer.yml

@@ -0,0 +1,37 @@
+name: fsanitizer
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-fsanitizer
+  cancel-in-progress: true
+
+jobs:
+  fsanitizer:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get submodules
+        run: |
+          git submodule update --init
+          cd external/Microphysics
+          git fetch; git checkout development
+          cd ../amrex
+          git fetch; git checkout development
+          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 subchandra
+        run: |
+          cd Exec/science/subchandra
+          make FSANITIZER=TRUE USE_MPI=FALSE -j 4
+
+      - name: Run subchandra
+        run: |
+          cd Exec/science/subchandra
+          ./Castro2d.gnu.SMPLSDC.ex inputs_2d.N14.coarse amr.max_level=1 max_step=1 amr.n_cell=320 640

.github/workflows/gh-pages.yml

@@ -44,7 +44,7 @@ jobs:
         run: ./deploy_docs_action.sh
 
       - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./out

.github/workflows/gpu_action.yml

@@ -1,6 +1,11 @@
 name: GPU compilation
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   gpu-compilation:
     runs-on: ubuntu-latest

.github/workflows/style/check_trailing_whitespaces.sh

@@ -6,6 +6,7 @@ find . -type d \( -name .git \
                   -o -path ./paper \
                   -o -name build -o -name install \
                   -o -name tmp_build_dir -o -name tmp_install_dir \
+                  -o -name ci-benchmarks \
                   -o -path ./util/gcem \
                \) -prune -o \
        -type f \( \( -name "*.H" -o -name "*.h" -o -name "*.hh" -o -name "*.hpp" \

.github/workflows/wdmerger_collision-compare.yml

@@ -1,6 +1,11 @@
 name: wdmerger_collision
 
 on: [pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
   wdmerger_collision-2d:
     runs-on: ubuntu-latest
@@ -43,5 +48,5 @@ jobs:
       - name: Check the extrema
         run: |
           cd Exec/science/wdmerger
-          ../../../external/amrex/Tools/Plotfile/fextrema.gnu.ex plt00095 > fextrema.out
+          ../../../external/amrex/Tools/Plotfile/fextrema.gnu.ex plt00086 > fextrema.out
           diff fextrema.out ci-benchmarks/wdmerger_collision_2D.out

CHANGES.md

@@ -1,3 +1,42 @@
+# 24.05
+
+  * Changed how the shock flag is computed.  It is now computed once,
+    at the start of a timestep.  It also takes into account sources
+    such that the pressure jump is only the pressure that is available
+    to drive a shock.  (#2726, #2728)
+
+  * Fixed a boundary condition check in gravity (#2833)
+
+  * Some coverity and clang-tidy fixes (#2810, #2811, #2835, #2831,
+    #2832)
+
+  * Fix the wdmerger initialization when the two stars are overlapping
+    (#2829)
+
+  * Fixed the Castro retry mechanism when amr.subcycling_mode = None
+    (#2821, #2824, #2826)
+
+  * Added more amr parameters to the job_info file (#2828)
+
+  * Added OpenMP to the SDC burn loop (#2770)
+
+# 24.04
+
+  * Some clang-tidy fixes (#2779, #2780, #2781, #2784, #2786, #2787, #2790,
+    #2791, #2792, #2793, #2797, #2798, #2799, #2800, #2801, #2804)
+
+  * Fix species initialization in the Detonation problem (#2806)
+    and let it work with NSE (#2765)
+
+  * Sync up with AMReX changes (#2794)
+
+  * wdmerger now reports composition of initial stars (#2767)
+
+  * flame_wave now checks if the `atm_delta` is too small (#2782)
+    and stores X(ash) (#2773)
+
+  * a bounds issue in the true SDC integration was fixed (#2775)
+
 # 24.03
 
   * Documentation updates (#2742, #2752, #2753)

Docs/source/debugging.rst

@@ -85,6 +85,12 @@ You can also use ask it to fix errors automatically via:
 
 and you can treat warnings as errors by adding ``CLANG_TIDY_WARN_ERROR=TRUE``.
 
+.. note::
+
+   Building a Castro problem with ``clang-tidy`` will suppress the
+   checks in AMReX and Microphysics sources and headers.  This is set by
+   the parameter ``CLANG_TIDY_IGNORE_SOURCES`` in ``Make.Castro``, and
+   the ``HeaderFilterRegex`` whitelist in ``.clang-tidy``.
 
 
 Thread sanitizer
@@ -121,5 +127,3 @@ to operate over.
 
 Physics issues
 ==============
-
-

Docs/source/io.rst

@@ -304,6 +304,8 @@ Derived variables
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | variable name                     | description                                       | derive routine              | units                                   |
 +===================================+===================================================+=============================+=========================================+
+| ``abar``                          | Mean atomic mass                                  | ``derabar``                 | :math:`\amu`                            |
++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | ``angular_momentum_x``,           | Angular momentum / volume in the x, y, or z dir   | ``derangmomx``,             | :math:`{\rm g~cm^{-1}~s^{-1}}`          |
 | ``angular_momentum_y``,           | computed as :math:`[(\rho \ub) \times {\bf r}]_n` | ``derangmomy``,             |                                         |
 | ``angular_momentum_z``            | where :math:`{\bf r}` is the distance from        | ``derangmomz``              |                                         |
@@ -328,6 +330,8 @@ Derived variables
 |                                   | :math:`s = s(\rho, e, X_k)`, where `e` is         |                             |                                         |
 |                                   | computed from :math:`(\rho e)`                    |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
+| ``enuc``                          | Nuclear energy generation rate / gram             | ``derenuc``                 | :math:`{\rm erg~g^{-1}~s^{-1}}`         |
++-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 | ``Ertot``                         | Total radiation energy density                    | ``derertot``                |                                         |
 |                                   | (for multigroup radiation problems)               |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
@@ -391,8 +395,6 @@ Derived variables
 | ``y_velocity``,                   | :math:`\ub = (\rho \ub)/\rho`                     |                             |                                         |
 | ``z_velocity``                    |                                                   |                             |                                         |
 +-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
-| ``enuc``                          | Nuclear energy generation rate / gram             | ``derenuc``                 | :math:`{\rm erg~g^{-1}~s^{-1}}`         |
-+-----------------------------------+---------------------------------------------------+-----------------------------+-----------------------------------------+
 
 problem-specific plotfile variables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^