Merge branch 'development' into lizmcole/Richardson-convergence-test-MHD

Author: lizmcole

.ci/azure-pipelines-amdgpu.yml

@@ -4,7 +4,30 @@
 # https://aka.ms/yaml
 
 trigger:
-- development
+  branches:
+    include:
+    - development
+  paths:
+    include:
+    - src/**
+    - tests/**
+    - inputs/**
+    - CMakeLists.txt
+    - .ci/azure-pipelines-amdgpu.yml
+    - extern/cooling/*.h5
+    - extern/amrex/**
+    - extern/Microphysics/**
+    - extern/fmt/**
+    - extern/yaml-cpp/**
+    - extern/openPMD-api/**
+    - extern/AMReX-Hydro/**
+    exclude:
+    - docs/**
+    - paper/**
+    - scripts/**
+    - '*.md'
+    - '*.rst'
+    - '*.txt'
 
 pr:
   autoCancel: true
@@ -13,20 +36,23 @@ pr:
     - development
   paths:
     include:
-    - src/*
-    - tests/*
-    - inputs/*
+    - src/**
+    - tests/**
+    - inputs/**
     - CMakeLists.txt
-    - .ci/*
-    - extern/amrex
-    - extern/Microphysics
-    - extern/fmt
-    - extern/yaml-cpp
-    - extern/openPMD-api
+    - .ci/azure-pipelines-amdgpu.yml
+    - extern/cooling/*.h5
+    - extern/amrex/**
+    - extern/Microphysics/**
+    - extern/fmt/**
+    - extern/yaml-cpp/**
+    - extern/openPMD-api/**
+    - extern/AMReX-Hydro/**
+    - extern/turbulence/**
     exclude:
-    - docs/*
-    - paper/*
-    - scripts/*
+    - docs/**
+    - paper/**
+    - scripts/**
     - '*.md'
     - '*.rst'
     - '*.txt'

.ci/azure-pipelines.yml

@@ -4,7 +4,29 @@
 # https://aka.ms/yaml
 
 trigger:
-- development
+  branches:
+    include:
+    - development
+  paths:
+    include:
+    - src/**
+    - inputs/**
+    - CMakeLists.txt
+    - .ci/azure-pipelines.yml
+    - extern/cooling/*.h5
+    - extern/amrex/**
+    - extern/Microphysics/**
+    - extern/fmt/**
+    - extern/yaml-cpp/**
+    - extern/openPMD-api/**
+    - extern/AMReX-Hydro/**
+    exclude:
+    - docs/**
+    - paper/**
+    - scripts/**
+    - '*.md'
+    - '*.rst'
+    - '*.txt'
 
 pr:
   autoCancel: true
@@ -13,19 +35,23 @@ pr:
     - development
   paths:
     include:
-    - src/*
-    - inputs/*
+    - src/**
+    - tests/**
+    - inputs/**
     - CMakeLists.txt
-    - .ci/*
-    - extern/amrex
-    - extern/Microphysics
-    - extern/fmt
-    - extern/yaml-cpp
-    - extern/openPMD-api
+    - .ci/azure-pipelines.yml
+    - extern/cooling/*.h5
+    - extern/amrex/**
+    - extern/Microphysics/**
+    - extern/fmt/**
+    - extern/yaml-cpp/**
+    - extern/openPMD-api/**
+    - extern/AMReX-Hydro/**
+    - extern/turbulence/**
     exclude:
-    - docs/*
-    - paper/*
-    - scripts/*
+    - docs/**
+    - paper/**
+    - scripts/**
     - '*.md'
     - '*.rst'
     - '*.txt'

.devcontainer/rocm-container/Dockerfile

@@ -20,30 +20,33 @@ RUN if ! zypper repos -E | grep devel_languages_perl; then \
     zypper clean --all && \
     cat rocm_so.conf >> /etc/ld.so.conf.d/rocm.conf && \
     rm rocm_so.conf && \
-    ldconfig
+	    ldconfig
 
 ENV PATH="/opt/rocm/bin:${PATH}" \
     LD_LIBRARY_PATH="/opt/rocm/lib:${LD_LIBRARY_PATH}"
 
-RUN zypper --non-interactive install wget tar gzip gcc gcc-fortran file gcc-c++ make && zypper clean --all && \
+COPY mpich-4.1.2-rocm-6.4-hip-pointer-attr.patch /tmp/mpich-4.1.2-rocm-6.4-hip-pointer-attr.patch
+
+RUN zypper --non-interactive install wget tar gzip gcc gcc-fortran file gcc-c++ make patch && zypper clean --all && \
     if [ ! -z "$(gcc --version | grep -Eo -m 1 [0-9][0-9]+\.[0-9]+\.[0-9]+ | grep -m 1 [0-9])" ]; then \
     export FFLAGS=-fallow-argument-mismatch; \
     fi && \
-    wget --progress=bar:force https://www.mpich.org/static/downloads/3.4.3/mpich-3.4.3.tar.gz && \
-    tar xzf mpich-3.4.3.tar.gz && \
-    cd mpich-3.4.3 && \
-    ./configure --with-device=ch4:ofi --prefix=/opt/mpich/3.4.3 --with-hip=/opt/rocm/hip && \
+    wget --progress=bar:force https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz && \
+    tar xzf mpich-4.1.2.tar.gz && \
+    cd mpich-4.1.2 && \
+    patch -p1 < /tmp/mpich-4.1.2-rocm-6.4-hip-pointer-attr.patch && \
+    ./configure --with-device=ch4:ofi --prefix=/opt/mpich/4.1.2 && \
     make install -j7 && \
     cd / && \
-    rm -rf mpich-3.4.3/ mpich-3.4.3.tar.gz
-
-ENV MPICH_VERSION="3.4.3" \
-    MPICH_URL="https://www.mpich.org/static/downloads/3.4.3/mpich-3.4.3.tar.gz" \
-    MPICH_DIR="/opt/mpich/3.4.3" \
-    PATH="/opt/mpich/3.4.3/bin:$PATH" \
-    LIBRARY_PATH="/opt/mpich/3.4.3/lib:$LIBRARY_PATH" \
-    LD_LIBRARY_PATH="/opt/mpich/3.4.3/lib:$LD_LIBRARY_PATH" \
-    MANPATH="/opt/mpich/3.4.3/share/man:$MANPATH"
+    rm -rf mpich-4.1.2/ mpich-4.1.2.tar.gz
+
+ENV MPICH_VERSION="4.1.2" \
+    MPICH_URL="https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz" \
+    MPICH_DIR="/opt/mpich/4.1.2" \
+    PATH="/opt/mpich/4.1.2/bin:$PATH" \
+    LIBRARY_PATH="/opt/mpich/4.1.2/lib:$LIBRARY_PATH" \
+    LD_LIBRARY_PATH="/opt/mpich/4.1.2/lib:$LD_LIBRARY_PATH" \
+    MANPATH="/opt/mpich/4.1.2/share/man:$MANPATH"
 
 # Install CMake
 RUN zypper --non-interactive install cmake && zypper clean --all

.devcontainer/rocm-container/mpich-4.1.2-rocm-6.4-hip-pointer-attr.patch

@@ -0,0 +1,19 @@
+diff --git a/src/mpl/src/gpu/mpl_gpu_hip.c b/src/mpl/src/gpu/mpl_gpu_hip.c
+index f6a2df3..b2c5954 100644
+--- a/src/mpl/src/gpu/mpl_gpu_hip.c
++++ b/src/mpl/src/gpu/mpl_gpu_hip.c
+@@ -90,7 +90,13 @@ int MPL_gpu_query_pointer_attr(const void *ptr, MPL_pointer_attr_t * attr)
+     hipError_t ret;
+     ret = hipPointerGetAttributes(&attr->device_attr, ptr);
+     if (ret == hipSuccess) {
+-        switch (attr->device_attr.memoryType) {
++#if defined(HIP_VERSION_MAJOR) && (HIP_VERSION_MAJOR >= 6)
++        /* ROCm 6+ uses hipPointerAttribute_t::type */
++        enum hipMemoryType memory_type = attr->device_attr.type;
++#else
++        enum hipMemoryType memory_type = attr->device_attr.memoryType;
++#endif
++        switch (memory_type) {
+             case hipMemoryTypeHost:
+                 attr->type = MPL_GPU_POINTER_REGISTERED_HOST;
+                 attr->device = attr->device_attr.device;

.dockerignore

@@ -0,0 +1,19 @@
+.git
+.gitmodules
+.github/workflows/**/node_modules
+.vscode
+
+# Local build artifacts
+build/
+cmake-build-*/
+
+# Large CI/regression assets (not needed for container builds)
+tests/
+
+# Developer-facing content (not needed for container builds)
+docs/
+paper/
+scripts/
+
+# OS/editor noise
+**/.DS_Store

.github/workflows/check_changes.yml

@@ -4,7 +4,7 @@ on:
   workflow_call:
     inputs:
       workflow_file:
-        description: 'Specific workflow file to check for changes (optional)'
+        description: "Specific workflow file to check for changes (optional)"
         required: false
         type: string
     outputs:
@@ -35,7 +35,7 @@ jobs:
       has_workflow_changes: ${{ steps.set-output.outputs.has_workflow_changes }}
       has_specific_workflow_changes: ${{ steps.set-output.outputs.has_specific_workflow_changes }}
     steps:
-      - uses: actions/checkout@v6.0.1
+      - uses: actions/checkout@v6
       - uses: dorny/paths-filter@v3
         id: changes
         with:
@@ -52,6 +52,7 @@ jobs:
               - 'extern/grackle_data_files/**'
               - 'extern/openPMD-api/**'
               - 'extern/yaml-cpp/**'
+              - 'extern/turbulence/**'
               - 'inputs/**'
               - 'CMakeLists.txt'
               - '**/*.cpp'

.github/workflows/clang-tidy-comments.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: ZedThree/clang-tidy-review/post@8e835e573551b213a7da2ccb4e9560a4785e46f4
+      - uses: ZedThree/clang-tidy-review/post@ec87cf75b3717b78d2c953c6530b6378467d5300
       # lgtm_comment_body, max_comments, and annotations need to be set on the posting workflow in a split setup
         with:
         # adjust options as necessary

.github/workflows/clang-tidy.yml

@@ -26,7 +26,7 @@ jobs:
         submodules: true
         fetch-depth: 0
 
-    - uses: ZedThree/clang-tidy-review@8e835e573551b213a7da2ccb4e9560a4785e46f4 # v0.22.2
+    - uses: ZedThree/clang-tidy-review@ec87cf75b3717b78d2c953c6530b6378467d5300 # v0.22.3
       id: review
       with:
         config_file: src/.clang-tidy
@@ -36,7 +36,7 @@ jobs:
         split_workflow: true
 
     # Uploads an artefact containing clang_fixes.json
-    - uses: ZedThree/clang-tidy-review/upload@8e835e573551b213a7da2ccb4e9560a4785e46f4 # v0.22.2
+    - uses: ZedThree/clang-tidy-review/upload@ec87cf75b3717b78d2c953c6530b6378467d5300 # v0.22.3
 
     # If there are any comments, fail the check
     - if: steps.review.outputs.total_comments > 0

.github/workflows/claude-code-review.yml

@@ -47,7 +47,7 @@ jobs:
 
       - name: Run Claude Code Review
         id: claude-review
-        uses: anthropics/claude-code-action@f0c8eb29807907de7f5412d04afceb5e24817127 # beta
+        uses: anthropics/claude-code-action@7145c3e0510bcdbdd29f67cc4a8c1958f1acfa2f # beta
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
 

.github/workflows/claude.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Run Claude Code
         id: claude
-        uses: anthropics/claude-code-action@f0c8eb29807907de7f5412d04afceb5e24817127 # beta
+        uses: anthropics/claude-code-action@7145c3e0510bcdbdd29f67cc4a8c1958f1acfa2f # beta
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}