Merge AMReX-Codes:development into ax3l:fix-pyproj-4

Author: EZoni

.github/workflows/dependencies/dependencies_clang6.sh renamed to .github/workflows/dependencies/dependencies_clang18.sh

@@ -11,4 +11,8 @@ sudo apt-get update
 
 sudo apt-get install -y  \
     build-essential      \
-    clang-6.0
+    clang-18             \
+    lld                  \
+    libc++-18-dev        \
+    libopenmpi-dev       \
+    openmpi-bin

.github/workflows/dependencies/gcc7.sh renamed to .github/workflows/dependencies/dependencies_gcc14.sh

@@ -11,6 +11,6 @@ sudo apt-get update
 
 sudo apt-get install -y --no-install-recommends\
     build-essential \
-    g++-7           \
+    g++-14          \
     libopenmpi-dev  \
     openmpi-bin

.github/workflows/dependencies/dependencies_nvcc11.sh renamed to .github/workflows/dependencies/dependencies_nvcc12.sh

@@ -16,8 +16,8 @@ sudo apt-get install -y \
     build-essential     \
     ca-certificates     \
     cmake               \
-    g++                 \
-    gfortran            \
+    g++-10              \
+    gfortran-10         \
     gnupg               \
     libopenmpi-dev      \
     openmpi-bin         \
@@ -29,12 +29,12 @@ echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x8
     | sudo tee /etc/apt/sources.list.d/cuda.list
 sudo apt-get update
 sudo apt-get install -y \
-    cuda-command-line-tools-11-2 \
-    cuda-compiler-11-2           \
-    cuda-cupti-dev-11-2          \
-    cuda-minimal-build-11-2      \
-    cuda-nvml-dev-11-2           \
-    cuda-nvtx-11-2               \
-    libcurand-dev-11-2           \
-    libcusparse-dev-11-2
-sudo ln -s cuda-11.2 /usr/local/cuda
+    cuda-command-line-tools-12-2 \
+    cuda-compiler-12-2           \
+    cuda-cupti-dev-12-2          \
+    cuda-minimal-build-12-2      \
+    cuda-nvml-dev-12-2           \
+    cuda-nvtx-12-2               \
+    libcurand-dev-12-2           \
+    libcusparse-dev-12-2
+sudo ln -s cuda-12.2 /usr/local/cuda

.github/workflows/dependencies/hip.sh

@@ -1,10 +1,15 @@
 #!/usr/bin/env bash
 #
-# Copyright 2022 The AMReX Community
+# Copyright 2020 The AMReX Community
 #
 # License: BSD-3-Clause-LBNL
 # Authors: Axel Huebl
 
+# search recursive inside a folder if a file contains tabs
+#
+# @result 0 if no files are found, else 1
+#
+
 set -eu -o pipefail
 
 # `man apt.conf`:
@@ -28,13 +33,16 @@ sudo apt-key add rocm.gpg.key
 
 source /etc/os-release # set UBUNTU_CODENAME: focal or jammy or ...
 
-echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${1-latest} ${UBUNTU_CODENAME} main" \
+VERSION=${1-6.3.2}
+
+echo "deb [arch=amd64] https://repo.radeon.com/rocm/apt/${VERSION} ${UBUNTU_CODENAME} main" \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
 
 # 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
@@ -46,25 +54,23 @@ sudo apt-get install -y --no-install-recommends \
     gfortran        \
     libnuma-dev     \
     libopenmpi-dev  \
-    ninja-build     \
     openmpi-bin     \
-    rocm-dev        \
-    rocfft-dev      \
-    rocprim-dev     \
-    rocrand-dev     \
-    rocsparse-dev   \
-    hiprand-dev
+    rocm-dev${VERSION}        \
+    roctracer-dev${VERSION}   \
+    rocprofiler-dev${VERSION} \
+    rocrand-dev${VERSION}     \
+    rocfft-dev${VERSION}      \
+    rocprim-dev${VERSION}     \
+    rocsparse-dev${VERSION}
+
+# hiprand-dev is a new package that does not exist in old versions
+sudo apt-get install -y --no-install-recommends hiprand-dev${VERSION} || true
 
 # activate
 #
 source /etc/profile.d/rocm.sh
 hipcc --version
+hipconfig --full
 which clang
 which clang++
-
-# cmake-easyinstall
-#
-sudo curl -L -o /usr/local/bin/cmake-easyinstall https://raw.githubusercontent.com/ax3l/cmake-easyinstall/main/cmake-easyinstall
-sudo chmod a+x /usr/local/bin/cmake-easyinstall
-export CEI_SUDO="sudo"
-export CEI_TMP="/tmp/cei"
+which flang

.github/workflows/hip.yml

@@ -8,8 +8,8 @@ concurrency:
 
 jobs:
   build_hip:
-    name: ROCm HIP 6.1
-    runs-on: ubuntu-20.04
+    name: ROCm HIP 6.3.2
+    runs-on: ubuntu-24.04
     env:
       CXXFLAGS: "-Werror -Wno-deprecated-declarations -Wno-error=pass-failed"
       CMAKE_GENERATOR: Ninja
@@ -18,7 +18,7 @@ jobs:
     - name: install dependencies
       shell: bash
       run: |
-        .github/workflows/dependencies/hip.sh 6.1
+        .github/workflows/dependencies/hip.sh 6.3.2
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -27,7 +27,7 @@ jobs:
         key: ccache-${{ github.workflow }}-${{ github.job }}-git-${{ github.sha }}
         restore-keys: |
              ccache-${{ github.workflow }}-${{ github.job }}-git-
-    - name: build ImpactX
+    - name: build pyAMReX
       shell: bash
       run: |
         export CCACHE_COMPRESS=1
@@ -46,15 +46,11 @@ jobs:
         python3 -m pip install -U build packaging setuptools[core] wheel
         python3 -m pip install -U cmake
 
-        # "mpic++ --showme" forgets open-pal in Ubuntu 20.04 + OpenMPI 4.0.3
-        #   https://bugs.launchpad.net/ubuntu/+source/openmpi/+bug/1941786
-        #   https://github.com/open-mpi/ompi/issues/9317
-        export LDFLAGS="-lopen-pal"
-
         cmake -S . -B build              \
             -DCMAKE_VERBOSE_MAKEFILE=ON  \
+            -DpyAMReX_IPO=OFF            \
             -DAMReX_GPU_BACKEND=HIP      \
-            -DAMReX_AMD_ARCH=gfx900      \
+            -DAMReX_AMD_ARCH=gfx90a      \
             -DAMReX_SPACEDIM="1;2;3"
         cmake --build build --target pip_install -j 4
 

.github/workflows/ubuntu.yml

@@ -8,12 +8,12 @@ concurrency:
 
 jobs:
   # Build and install libamrex as AMReX CMake project
-  gcc7:
-    name: GNU@7.5
-    runs-on: ubuntu-20.04
+  gcc10:
+    name: GNU@10.5 Release
+    runs-on: ubuntu-24.04
     env:
-      CC: gcc-7
-      CXX: g++-7
+      CC: gcc-10
+      CXX: g++-10
       CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wunreachable-code -fno-operator-names -Wno-array-bounds"
     steps:
     - uses: actions/checkout@v4
@@ -23,7 +23,7 @@ jobs:
         python-version: '3.9'
     - name: Dependencies
       run: |
-        .github/workflows/dependencies/gcc7.sh
+        .github/workflows/dependencies/dependencies_gcc10.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -56,15 +56,15 @@ jobs:
       run: |
         mpiexec -np 1 python3 -m pytest tests/
 
-  gcc10:
-    name: GNU@10.5 Debug
-    runs-on: ubuntu-22.04
+  gcc14:
+    name: GNU@14.5 Debug
+    runs-on: ubuntu-24.04
     env: {CXXFLAGS: "-Werror -Wno-error=deprecated-declarations -Wshadow -Woverloaded-virtual -Wunreachable-code -fno-operator-names"}
     steps:
     - uses: actions/checkout@v4
     - name: Dependencies
       run: |
-        .github/workflows/dependencies/dependencies_gcc10.sh
+        .github/workflows/dependencies/dependencies_gcc14.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -80,8 +80,8 @@ jobs:
         export CCACHE_MAXSIZE=600M
         ccache -z
 
-        export CC=$(which gcc-10)
-        export CXX=$(which g++-10)
+        export CC=$(which gcc-14)
+        export CXX=$(which g++-14)
         python3 -m pip install -U pip
         python3 -m pip install -U build packaging setuptools[core] wheel
         python3 -m pip install -U cmake
@@ -108,15 +108,15 @@ jobs:
         rm -rf build
         python3 -m pytest tests
 
-  clang6:
-    name: Clang@6.0 w/o MPI
-    runs-on: ubuntu-20.04
+  clang14:
+    name: Clang@14.0 w/o MPI
+    runs-on: ubuntu-24.04
     env: {CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -fno-operator-names -Wno-pass-failed"}
     steps:
     - uses: actions/checkout@v4
     - name: Dependencies
       run: |
-        .github/workflows/dependencies/dependencies_clang6.sh
+        .github/workflows/dependencies/dependencies_clang14_libcpp.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -134,8 +134,8 @@ jobs:
 
         export CMAKE_BUILD_PARALLEL_LEVEL=4
 
-        export CC=$(which clang-6.0)
-        export CXX=$(which clang++-6.0)
+        export CC=$(which clang-14)
+        export CXX=$(which clang++-14)
         python3 -m pip install -U pip
         python3 -m pip install -U build packaging setuptools[core] wheel
         python3 -m pip install -U cmake pytest
@@ -151,9 +151,9 @@ jobs:
       run: |
         python3 -m pytest tests/
 
-  clang14:
-    name: Clang@14.0 w/ libc++ w/ MPI
-    runs-on: ubuntu-22.04
+  clang18:
+    name: Clang@18.0 w/ libc++ w/ MPI
+    runs-on: ubuntu-24.04
     env:
       CXXFLAGS: "-Werror -Wshadow -Woverloaded-virtual -Wextra-semi -Wunreachable-code -fno-operator-names -Wno-pass-failed -stdlib=libc++"
       LDFLAGS: "-fuse-ld=lld"
@@ -163,7 +163,7 @@ jobs:
     - uses: actions/checkout@v4
     - name: Dependencies
       run: |
-        .github/workflows/dependencies/dependencies_clang14_libcpp.sh
+        .github/workflows/dependencies/dependencies_clang18.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -181,6 +181,8 @@ jobs:
 
         export CMAKE_BUILD_PARALLEL_LEVEL=4
 
+        export CC=$(which clang-18)
+        export CXX=$(which clang++-18)
         python3 -m pip install -U pip
         python3 -m pip install -U build packaging setuptools[core] wheel
         python3 -m pip install -U cmake
@@ -198,14 +200,14 @@ jobs:
         python3 -m pytest tests/
 
   nvcc11:
-    name: CUDA@11.2 GNU@9.4.0
-    runs-on: ubuntu-20.04
+    name: CUDA@12.2 GNU@10.5
+    runs-on: ubuntu-24.04
     env: {CXXFLAGS: "-fno-operator-names"}
     steps:
     - uses: actions/checkout@v4
     - name: Dependencies
       run: |
-        .github/workflows/dependencies/dependencies_nvcc11.sh
+        .github/workflows/dependencies/dependencies_nvcc12.sh
         .github/workflows/dependencies/dependencies_ccache.sh
     - name: Set Up Cache
       uses: actions/cache@v4
@@ -225,9 +227,9 @@ jobs:
         export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda/lib64:${LD_LIBRARY_PATH}
         which nvcc || echo "nvcc not in PATH!"
 
-        export CC=$(which gcc)
-        export CXX=$(which g++)
-        export CUDAHOSTCXX=$(which g++)
+        export CC=$(which gcc-10)
+        export CXX=$(which g++-10)
+        export CUDAHOSTCXX=$(which g++-10)
 
         python3 -m pip install -U pip
         python3 -m pip install -U build packaging setuptools[core] wheel

.pre-commit-config.yaml

@@ -74,7 +74,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.2
+  rev: v0.11.8
   hooks:
     # Run the linter
     - id: ruff

cmake/dependencies/AMReX.cmake

@@ -86,7 +86,7 @@ option(pyAMReX_amrex_internal "Download & build AMReX" ON)
 set(pyAMReX_amrex_repo "https://github.com/AMReX-Codes/amrex.git"
     CACHE STRING
     "Repository URI to pull and build AMReX from if(pyAMReX_amrex_internal)")
-set(pyAMReX_amrex_branch "25.04"
+set(pyAMReX_amrex_branch "793ea9f717590d66d178a86298b82aac244b77a7"
     CACHE STRING
     "Repository branch for pyAMReX_amrex_repo if(pyAMReX_amrex_internal)")
 

src/Base/BoxArray.cpp

@@ -120,30 +120,27 @@ void init_BoxArray(py::module &m) {
     //! \brief Grow each Box in the BoxArray on the high end
     //! by n_cell cells in the idir direction.
     BoxArray& growHi (int idir, int n_cell);
-    //! \brief Apply surroundingNodes(Box) to each Box in BoxArray.
-    //! See the documentation of Box for details.
-    BoxArray& surroundingNodes ();
-    //!
+*/
+
     //! \brief Apply surroundingNodes(Box,int) to each Box in
     //! BoxArray.  See the documentation of Box for details.
-    BoxArray& surroundingNodes (int dir);
-*/
+    .def("surroundingNodes",
+            py::overload_cast<>(&BoxArray::surroundingNodes))
+    .def("surroundingNodes",
+            py::overload_cast<int>(&BoxArray::surroundingNodes))
 
     //! Apply Box::enclosedCells() to each Box in the BoxArray.
     .def("enclosed_cells",
             py::overload_cast<>(&BoxArray::enclosedCells))
     .def("enclosed_cells",
             py::overload_cast<int>(&BoxArray::enclosedCells))
 
+    //! Convert nodality of each box in the BoxArray
+    .def("convert",
+            py::overload_cast< IndexType >(&BoxArray::convert))
+    .def("convert",
+            py::overload_cast< IntVect const &>(&BoxArray::convert))
 /*
-    //! Apply Box::convert(IndexType) to each Box in the BoxArray.
-    BoxArray& convert (IndexType typ);
-
-    BoxArray& convert (const IntVect& typ);
-
-    //! Apply function (*fp)(Box) to each Box in the BoxArray.
-    BoxArray& convert (Box (*fp)(const Box&));
-
     //! Apply Box::shift(int,int) to each Box in the BoxArray.
     BoxArray& shift (int dir, int nzones);