Merge branch 'development' into retry_retry

.editorconfig

@@ -0,0 +1,62 @@
+# 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
+
+[networks/**/reaclib_rates.H]
+# some reaclib rate labels have trailing spaces
+trim_trailing_whitespace = false
+
+
+[*.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
+
+
+[util/gcem/**]
+# don't mess with the gcem subtree
+indent_style = unset
+indent_size = unset
+trim_trailing_whitespace = unset
+end_of_line = unset
+insert_final_newline = unset

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Replaced tabs with spaces and trimmed trailing whitespace
+5a2247f598f88f80ad8b186188fccfd5537b18d3

.github/workflows/burn_cell.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Compare to stored output (VODE, subch_approx)
         run: |
           cd unit_test/burn_cell
-          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_unit_test.out
 
       - name: Compile, burn_cell (VODE, ECSN)
         run: |
@@ -53,10 +53,42 @@ jobs:
           cd unit_test/burn_cell
           ./main3d.gnu.ex inputs_ecsn > test.out
 
-      - name: Compare to stored output (ECSN)
+      - name: Compare to stored output (VODE, ECSN)
         run: |
           cd unit_test/burn_cell
-          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ecsn_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/ecsn_unit_test.out
+
+      - name: Compile, burn_cell (VODE, ignition_chamulak)
+        run: |
+          cd unit_test/burn_cell
+          make realclean
+          make NETWORK_DIR=ignition_chamulak -j 4
+
+      - name: Run burn_cell (VODE, ignition_chamulak)
+        run: |
+          cd unit_test/burn_cell
+          ./main3d.gnu.ex inputs_ignition_chamulak > test.out
+
+      - name: Compare to stored output (VODE, ignition_chamulak)
+        run: |
+          cd unit_test/burn_cell
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/chamulak_VODE_unit_test.out
+
+      - name: Compile, burn_cell (ForwardEuler, triple_alpha_plus_cago)
+        run: |
+          cd unit_test/burn_cell
+          make realclean
+          make NETWORK_DIR=triple_alpha_plus_cago INTEGRATOR_DIR=ForwardEuler -j 4
+
+      - name: Run burn_cell (ForwardEuler, triple_alpha_plus_cago)
+        run: |
+          cd unit_test/burn_cell
+          ./main3d.gnu.ex inputs_triple > test.out
+
+      - name: Compare to stored output (ForwardEuler, triple_alpha_plus_cago)
+        run: |
+          cd unit_test/burn_cell
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/triple_alpha_plus_cago_FE_unit_test.out
 
       - name: Compile, burn_cell (BackwardEuler, subch_approx)
         run: |
@@ -72,7 +104,7 @@ jobs:
       - name: Compare to stored output (BackwardEuler, subch_approx)
         run: |
           cd unit_test/burn_cell
-          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_BE_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/subch_approx_BE_unit_test.out
 
       - name: Compile, burn_cell (QSS, aprox13)
         run: |
@@ -88,7 +120,7 @@ jobs:
       - name: Compare to stored output (QSS, aprox13)
         run: |
           cd unit_test/burn_cell
-          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_QSS_unit_test.out
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_QSS_unit_test.out
 
       - name: Compile, burn_cell (RKC, aprox13)
         run: |
@@ -99,11 +131,9 @@ jobs:
       - name: Run burn_cell (RKC, aprox13)
         run: |
           cd unit_test/burn_cell
-          ./main3d.gnu.ex inputs_aprox13 unit_test.temperature=2.e9 > test.out
+          ./main3d.gnu.ex inputs_aprox13 unit_test.temperature=1.e9 > test.out
 
       - name: Compare to stored output (RKC, aprox13)
         run: |
           cd unit_test/burn_cell
-          diff -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out
-
-
+          diff -I "^Initializing AMReX" -I "^AMReX" -I "^reading in reaclib rates" test.out ci-benchmarks/aprox13_RKC_unit_test.out

.github/workflows/burn_cell_primordial_chem.yml

@@ -47,7 +47,7 @@ jobs:
             value2=$(awk 'NR=='"$line_number"' {match($0, /[+-]?[0-9]+([.][0-9]+)?[eE]?[+-]?[0-9]+/); if (RSTART) print substr($0, RSTART, RLENGTH)}' reference_solution.out)
 
             difference=$(awk -v val1="$value1" -v val2="$value2" 'BEGIN { printf "%.2f", (val1 - val2) / val2 }')
-            
+
             if (( $(echo "$difference > $threshold" | bc -l) )); then
               echo "Line number: $line_number"
               echo "Value in test.out: $value1"

.github/workflows/c-linter.yml

@@ -22,19 +22,16 @@ jobs:
           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 clang-tidy cmake jq clang cppcheck clang-format bear g++>=9.3.0
-
       - name: Run cpp linter
         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'
-          ignore_files: 'amrex'
+          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
+          # not sure why cppcheck tests _MSC_VER, since it's only referenced from gcem
+          cppcheck_options: '-U_OPENMP -UAMREX_USE_GPU -UAMREX_USE_CUDA -UAMREX_USE_HIP -U_MSC_VER'
 
       - name: Archive clang tidy report
         uses: actions/upload-artifact@v1

.github/workflows/castro.yml

@@ -0,0 +1,89 @@
+name: Castro
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.head_ref }}-apps
+  cancel-in-progress: true
+
+jobs:
+  castro:
+    name: Castro
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Get Latest Release Tag
+      run: |
+        AMREX_TAG=$(wget https://github.com/AMReX-Codes/amrex/releases/latest 2>&1 | grep Location: | awk '{print $2}' | awk -F/ '{print $NF}')
+        echo "AMREX_TAG=$AMREX_TAG" >> $GITHUB_ENV
+    - name: Download Castro
+      uses: actions/checkout@v3
+      with:
+        repository: 'AMReX-Astro/Castro'
+        ref: development
+        path: 'Castro'
+    - name: Download AMReX
+      uses: actions/checkout@v3
+      with:
+        repository: 'AMReX-Codes/amrex'
+        ref: ${{env.AMREX_TAG}}
+        path: 'amrex'
+    - name: Dependencies
+      run: |
+        .github/workflows/dependencies/dependencies.sh
+        .github/workflows/dependencies/dependencies_ccache.sh
+    - name: Set Up Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/ccache
+        key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
+        restore-keys: |
+             ccache-${{ github.workflow }}-${{ github.job }}-git-
+    - name: Build flame_wave
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/flame_wave/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+    - name: Build subchandra
+      run: |
+        export CCACHE_COMPRESS=1
+        export CCACHE_COMPRESSLEVEL=10
+        export CCACHE_MAXSIZE=75M
+        export CCACHE_LOGFILE=${{ github.workspace }}/ccache.log.txt
+        ccache -z
+
+        export AMREX_HOME=${PWD}/amrex
+        export MICROPHYSICS_HOME=${PWD}
+
+        cd Castro/Exec/science/subchandra/
+        make -j2 CCACHE=ccache USE_MPI=FALSE
+
+        ccache -s
+        du -hs ~/.cache/ccache
+
+  save_pr_number:
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Save PR number
+        env:
+          PR_NUMBER: ${{ github.event.number }}
+        run: |
+          echo $PR_NUMBER > pr_number.txt
+      - uses: actions/upload-artifact@v3
+        with:
+          name: pr_number
+          path: pr_number.txt
+          retention-days: 1

.github/workflows/cmake_build_cell_primordial_chem.yml

@@ -17,6 +17,6 @@ jobs:
       - name: Compile and run
         run: |
           mkdir build && cd build
-          cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMREX=true
+          cmake .. -DBUILD_UNIT_TEST=true -DBUILD_AMReX=true
           make -j2
           ctest --output-on-failure

.github/workflows/create_release.yml

@@ -2,8 +2,8 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-      - '[0-9][0-9].[0-9][0-9]' 
-  
+      - '[0-9][0-9].[0-9][0-9]'
+
 name: Create Release
 
 jobs:

.github/workflows/cuda.yml

@@ -26,17 +26,23 @@ jobs:
           cd ../..
 
       - name: Dependencies
-        run: .github/workflows/dependencies_nvcc11.sh
+        run: .github/workflows/dependencies/dependencies_nvcc11.sh
 
       - 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
 
-      - name: compile test_react (subch_simple)
+      - name: compile test_react (ignition_reaclib/URCA-simple)
         run: |
           export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
           cd unit_test/test_react
           make realclean
-          make NETWORK_DIR=subch_simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+          make NETWORK_DIR=ignition_reaclib/URCA-simple USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2
+
+      - name: compile test_ase (ase)
+        run: |
+          export PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:${PATH}
+          cd unit_test/test_ase
+          make USE_CUDA=TRUE COMP=gnu USE_MPI=FALSE -j 2

.github/workflows/dependencies/dependencies.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+#
+# Copyright 2020-2022 The AMReX Community
+#
+# License: BSD-3-Clause-LBNL
+# Authors: Axel Huebl
+
+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 update
+
+sudo apt-get install -y --no-install-recommends\
+    build-essential \
+    g++ gfortran    \
+    libopenmpi-dev  \
+    openmpi-bin

.github/workflows/dependencies/dependencies_ccache.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+if [[ $# -eq 2 ]]; then
+  CVER=$1
+else
+  CVER=4.8
+fi
+
+wget https://github.com/ccache/ccache/releases/download/v${CVER}/ccache-${CVER}-linux-x86_64.tar.xz
+tar xvf ccache-${CVER}-linux-x86_64.tar.xz
+sudo cp -f ccache-${CVER}-linux-x86_64/ccache /usr/local/bin/

.github/workflows/eos_cell.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Compare to stored output (helmholtz)
         run: |
           cd unit_test/eos_cell
-          diff -I "^AMReX" test.out ci-benchmarks/eos_helmholtz.out
+          diff -I "^Initializing AMReX" -I "^AMReX" test.out ci-benchmarks/eos_helmholtz.out
 
       - name: Compile eos_cell (gamma_law)
         run: |
@@ -56,6 +56,6 @@ jobs:
       - name: Compare to stored output (gamma_law)
         run: |
           cd unit_test/eos_cell
-          diff -I "^AMReX" test.out ci-benchmarks/eos_gamma_law.out
+          diff -I "^Initializing AMReX" -I "^AMReX" test.out ci-benchmarks/eos_gamma_law.out
 
 

.github/workflows/find_changed_files.py

@@ -28,17 +28,17 @@ def find_files(SHAs=None):
     if stderr is not None:
         raise Exception('git diff encountered an error')
 
-    files = [f for f in stdout.decode('utf-8').strip().split('\n') 
+    files = [f for f in stdout.decode('utf-8').strip().split('\n')
              if f.startswith('networks/')]
     print(files)
 
     # see which directories contain changed files
     changed_networks = set()
     for f in files:
-        # check for the NETWORK_PROPERTIES file in each parent directory
+        # check for the actual_network.H file in each parent directory
         parts = f.split('/')
         while parts:
-            if os.path.exists(os.path.join(*parts, 'NETWORK_PROPERTIES')):
+            if os.path.exists(os.path.join(*parts, 'actual_network.H')):
                 # remove networks/
                 changed_networks.add(os.path.join(*parts[1:]))
                 break