Merge branch 'development' into clang-tidy-header

.clang-tidy

@@ -13,7 +13,6 @@ Checks: >
        -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-*,
@@ -25,9 +24,9 @@ Checks: >
      modernize-*,
        -modernize-avoid-c-arrays,
        -modernize-use-trailing-return-type,
-       -modernize-use-using,
      performance-*,
        -performance-avoid-endl,
+       -performance-enum-size,
      portability-*,
      readability-*,
        -readability-avoid-const-params-in-decls,
@@ -40,6 +39,8 @@ Checks: >
        -readability-isolate-declaration,
        -readability-magic-numbers,
        -readability-named-parameter,
+       -readability-redundant-inline-specifier,
+       -readability-redundant-member-init,
        -readability-simplify-boolean-expr,
        -readability-static-accessed-through-instance,
      mpi-*,

.codespell-ignore-words

@@ -12,3 +12,4 @@ nd
 ue
 bion
 aas
+checkin

.editorconfig

@@ -0,0 +1,49 @@
+# http://EditorConfig.org
+#
+# precedence of rules is bottom to top
+
+# this is the top-most EditorConfig file
+root = true
+
+
+[*.{c,h,cpp,hpp,H,py}]
+# 4 space indentation
+indent_style = space
+indent_size = 4
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+# unix-style newlines
+end_of_line = lf
+
+# newline ending in files
+insert_final_newline = true
+
+
+[*.md]
+# two end of line whitespaces are newlines without a paragraph
+trim_trailing_whitespace = false
+
+
+[*.rst]
+# Enforce UTF-8 encoding
+charset = utf-8
+
+# Unix-style newlines
+end_of_line = lf
+
+# Newline ending in files
+insert_final_newline = true
+
+# 3 space indentation
+indent_style = space
+indent_size = 3
+
+# Clean up trailing whitespace
+trim_trailing_whitespace = true
+
+[{Makefile,GNUmakefile,Make.*}]
+# TABs are part of its syntax
+indent_style = tab
+indent_size = unset

.github/workflows/check_params.py

@@ -48,7 +48,7 @@ def doit(castro_dir):
                 # remove comments
                 idx = line.find("#")
                 if idx > 0:
-                    line = line[idx:]
+                    line = line[:idx]
 
                 found_param = pattern.match(line)
                 if not found_param:

.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/dependencies_hip.sh

@@ -17,10 +17,23 @@ set -eu -o pipefail
 #   failed files the given number of times.
 echo 'Acquire::Retries "3";' | sudo tee /etc/apt/apt.conf.d/80-retries
 
-# Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
+# Ref.: https://rocm.docs.amd.com/projects/install-on-linux/en/latest/how-to/native-install/ubuntu.html
+
+# Make the directory if it doesn't exist yet.
+# This location is recommended by the distribution maintainers.
+sudo mkdir --parents --mode=0755 /etc/apt/keyrings
+
+# Download the key, convert the signing-key to a full
+# keyring required by apt and store in the keyring directory
+wget https://repo.radeon.com/rocm/rocm.gpg.key -O - | \
+    gpg --dearmor | sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
+
 curl -O https://repo.radeon.com/rocm/rocm.gpg.key
 sudo apt-key add rocm.gpg.key
-echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-debian}/ ubuntu main" \
+
+source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
@@ -43,8 +56,10 @@ sudo apt-get install -y --no-install-recommends \
     roctracer-dev   \
     rocprofiler-dev \
     rocrand-dev     \
-    rocprim-dev     \
-    hiprand-dev
+    rocprim-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
 
 # activate
 #

.github/workflows/flame_wave-compare.yml

@@ -36,7 +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: |
@@ -47,3 +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/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/good_defines.txt

@@ -1,3 +1,4 @@
+ALLOW_GPU_PRINTF
 AMREX_DEBUG
 AMREX_PARTICLES
 AMREX_SPACEDIM

.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

@@ -48,5 +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

.zenodo.json

@@ -17,6 +17,11 @@
             "name": "Bell, John",
             "orcid": "0000-0002-5749-334X"
         },
+        {
+            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Chen, Zhi",
+            "orcid": "0000-0002-2839-107X"
+        },
         {
             "name": "Harpole, Alice",
             "orcid": "0000-0002-1530-781X"

CHANGES.md

@@ -1,3 +1,109 @@
+# 24.09
+
+  * Code clean-ups / clang-tidy (#2942, #2949)
+
+  * update the `hse_convergence` readme to reflect current convergence
+    (#2946)
+
+  * update the `bubble_convergence` plotting script (#2947)
+
+  * new Frontier scaling numbers (#2948)
+
+  * more GPU error printing (@3944)
+
+  * science problem updates: `flame_wave` (#2943)
+
+  * documentation updates (#2939)
+
+# 24.08
+
+  * lazy QueueReduction has been enabled for the timing diagnostics
+    (#2926)
+
+  * The `job_info` file output now correctly labels the compute time
+    as GPU-hours instead of CPU-hours when running on GPUs (#2930)
+
+  * We can now output warnings when running on GPUs if you build
+    with `USE_GPU_PRINTF=TRUE`(#2923, #2928)
+
+  * Code clean-ups / sync with Microphysics (#2900, #2901, #2905,
+    #2906, #2909, #2912, #2919, #2922, #2932, #2933, #2936, #2938,
+    #2940)
+
+  * The area weighting in the diagnostics in `subch_planar` was fixed
+    (#2885)
+
+  * A script to produce a resolution study for the `circular_det`
+    problem was added (#2857)
+
+  * science problem updates: `xrb_layered` (#2917), `nova` (#2913),
+    `wdmerger` (#2907, #2918, #2931), `Detonation` (#2902)
+
+  * updated scaling results on Frontier (#2904, #2914, #2915)
+
+  * more exact Riemann solver clean-up (#2896, #2897, #2898)
+    and clean-ups to the two shock solvers (#2895)
+
+  * fix issues with eigenvectors and clang-tidy in the MHD solver
+    (#2880)
+
+# 24.07
+
+  * Reorganizing of the existing 2-shock and HLL Riemann solvers
+    (#2887, #2888, #2889, #2890)
+
+  * Some clean-up, accuracy improvements, and optimization of the
+    exact Riemann solver in preparation for coupling it to simulations
+    (#2868, #2869, #2875)
+
+  * a new problem setup, `subch_planar`, for exploring He detonations
+    (#2870, #2873, #2881, #2883, #2886, #2877, #2878)
+
+  * clean-up the computation of the shock variable for hybrid Riemann
+    solves (#2865)
+
+  * code clean-ups (#2852, #2871, #2891)
+
+  * documentation improvements (#2843, #2879)
+
+  * add an EditorConfig (#2872)
+
+  * add the circular detonation problem to test multidimensional shock
+    algorithms (#2858)
+
+# 24.06
+
+  * Doc updates (#2839, #2842, #2846, #2851, #2854, #2860)
+
+  * Sync problem and Castro runtime parameters to recent Microphysics
+    changes (#2838, #2845, #2861)
+
+  * fix parsing in the `check_params.py` script (#2850)
+
+  * code cleaning (#2840, #2842, #2843)
+
+# 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,

Diagnostics/DustCollapse/GNUmakefile

@@ -10,8 +10,6 @@ USE_OMP = FALSE
 
 USE_REACT = FALSE
 
-USE_ACC = FALSE
-
 # programs to be compiled
 ALL: dustcollapse_$(DIM)d.ex
 

Diagnostics/Radiation/GNUmakefile

@@ -10,8 +10,6 @@ USE_OMP = FALSE
 
 USE_REACT = FALSE
 
-USE_ACC = FALSE
-
 ALL: radhelp
 
 radhelp:

Diagnostics/Sedov/GNUmakefile

@@ -10,8 +10,6 @@ USE_OMP = FALSE
 
 USE_REACT = FALSE
 
-USE_ACC = FALSE
-
 # programs to be compiled
 ALL: sedov_$(DIM)d.ex
 

Docs/source/Hydrodynamics.rst

@@ -609,7 +609,7 @@ behavior:
 Compute Primitive Variables
 ---------------------------
 
-We compute the primtive variables from the conserved variables.
+We compute the primitive variables from the conserved variables.
 
 -  :math:`\rho, \rho e`: directly copy these from the conserved state
    vector

Docs/source/Verification.rst

@@ -495,7 +495,7 @@ test problem. A hot sphere is centered at the origin in a spherical
 geometry. The spectrum from this sphere follows a Planck
 distribution. The ambient medium is at a much lower temperature. A
 frequency-dependent opacity makes the domain optically thin for high
-frequecies and optically thick for low frequency. At long times, the
+frequencies and optically thick for low frequency. At long times, the
 solution will be a combination of the blackbody radiation from the
 ambient medium plus the radiation that propagated from the hot sphere.
 An analytic solution exists :cite:`graziani:2008` which gives the

Docs/source/conf.py

@@ -82,7 +82,7 @@ def get_version():
 
 # General information about the project.
 project = 'Castro'
-copyright = '2018-2022, Castro development team'
+copyright = '2018-2024, Castro development team'
 author = 'Castro development team'
 
 html_logo = "castro_logo_hot_200.png"
@@ -218,6 +218,12 @@ def get_version():
 ]
 
 
+# -- Options for linkcheck
+
+linkcheck_retries = 3
+linkcheck_timeout = 100
+
+
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples