Merge branch 'development' into ice

Author: zingale

.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