docker

Signed-off-by: Jean-Michel Batto <jmbatto@gmail.com>

docker/Dockerfile

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+FROM debian:trixie-slim
+
+# Metadata
+LABEL maintainer="jmbatto"
+LABEL description="Julia 1.12 (Source Build) on Debian Trixie with PDI/GTK - Optimized for stability"
+
+# Build Arguments
+ARG USER_ID=1001
+ARG GROUP_ID=1001
+ARG USER_NAME=coder
+ARG JULIA_VERSION=v1.12.4
+ARG PDI_VERSION=1.10.0
+
+# -----------------------------------------------------------------------------
+# 1. System Dependencies Installation
+# -----------------------------------------------------------------------------
+# Rationale:
+# - 'neowofetch': Replaces 'neofetch' which has been removed from Debian Trixie repos.
+# - 'python3-setuptools': REQUIRED for PDI compilation. Python 3.12+ (shipped with Trixie)
+#   removed 'distutils', causing CMake/PDI detection scripts to fail without setuptools.
+# - 'dbus-x11' & 'xvfb': Essential for running GTK applications in a headless Docker environment.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    # Build tools and base utilities
+    build-essential cmake git pkg-config \
+    gfortran which perl gawk m4 vim libatomic1 \
+    nano sudo lsof jq neowofetch curl wget \
+    gdb valgrind clang-format \
+    ca-certificates iputils-ping colordiff \
+    # Python Environment (with setuptools fix for Py3.12)
+    python3 python3-dev python3-numpy python3-pandas python3-matplotlib python3-pip python3-h5py python3-termcolor python3-setuptools \
+    # Scientific Libraries (MPI/PDI/HDF5)
+    mpi-default-dev libhdf5-dev libz-dev hdf5-tools \
+    # Graphics Stack (X11, GTK4, OpenGL, DBus)
+    libx11-6 libxext6 libxrender1 libxtst6 xauth xvfb dbus-x11 \
+    libgl1-mesa-dri libgl1 \
+    libgtk-4-1 libgtk-3-0 libglib2.0-0 libcairo2 \
+    libpango-1.0-0 libharfbuzz0b \
+    libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-bin \
+    libgraphene-1.0-0 librsvg2-common \
+    shared-mime-info \
+    adwaita-icon-theme-full hicolor-icon-theme fonts-liberation \
+    graphviz \
+    && rm -rf /var/lib/apt/lists/*
+
+# Fix: Generate machine-id to prevent GLib/GTK runtime errors regarding missing D-Bus UUID.
+RUN dbus-uuidgen > /etc/machine-id
+
+# Fix: Update GDK pixbuf loaders cache.
+# Prevents runtime warnings/errors about missing image format loaders.
+RUN LOADER_PATH=$(find /usr/lib -name gdk-pixbuf-query-loaders | head -n 1) && \
+    ln -s $LOADER_PATH /usr/bin/gdk-pixbuf-query-loaders && \
+    gdk-pixbuf-query-loaders --update-cache
+
+# -----------------------------------------------------------------------------
+# 2. JULIA COMPILATION
+# -----------------------------------------------------------------------------
+WORKDIR /tmp/julia-build
+RUN git clone --depth 1 --branch ${JULIA_VERSION} https://github.com/JuliaLang/julia.git .
+
+# Build Configuration (Make.user) - CRITICAL FIXES FOR DEBIAN TRIXIE
+# 1. USE_SYSTEM_LIBUNWIND=0: Forces internal libunwind. System libunwind on Trixie causes Segfaults.
+# 2. noexecstack: Security flag required by modern Linux kernels.
+# 3. -gdwarf-4: CRITICAL FIX. GCC 13+ defaults to DWARF-5 debug format, which is incompatible
+#    with Julia's current unwinder, leading to immediate Segfaults on startup.
+RUN echo "prefix=/usr/local/julia" > Make.user && \
+    echo "MARCH=x86-64" >> Make.user && \
+    echo "USE_SYSTEM_LIBUNWIND=0" >> Make.user && \
+    echo "LDFLAGS=-Wl,-z,noexecstack" >> Make.user && \
+    echo "CFLAGS=-Wa,--noexecstack -gdwarf-4" >> Make.user && \
+    echo "CXXFLAGS=-Wa,--noexecstack -gdwarf-4" >> Make.user
+
+# Compile, Install, and Cleanup
+# Cleanup is performed immediately to reduce final image size (~1GB saved).
+ENV JULIA_PATH=/usr/local/julia
+ENV PATH=$JULIA_PATH/bin:$PATH
+RUN make -j$(nproc) && \
+    make install && \
+    rm -rf /tmp/julia-build
+
+# -----------------------------------------------------------------------------
+# 3. PDI INSTALLATION
+# -----------------------------------------------------------------------------
+ENV PDI_DIR=/usr/local
+ENV LD_LIBRARY_PATH=/usr/local/lib:/usr/lib/x86_64-linux-gnu
+ENV CPATH=/usr/local/include
+ENV PREFIX=/usr/local
+
+WORKDIR /tmp/pdi-build
+# Build Configuration:
+# - BUILD_PYTHON=ON & BUILD_PYCALL_PLUGIN=ON: Explicitly enabled to generate
+#   'libpdi_pycall_plugin.so'. Required to prevent 'plugin not found' errors
+#   when interacting with Python from Julia/PDI.
+RUN git clone --depth 1 --branch ${PDI_VERSION} https://github.com/pdidev/pdi.git . && \
+    mkdir build && cd build && \
+    cmake \
+        -DBUILD_MPI=OFF \
+        -DBUILD_DECL_HDF5_PLUGIN=ON \
+        -DBUILD_SHARED_LIBS=ON \
+        -DBUILD_FORTRAN=OFF \
+        -DBUILD_HDF5_PARALLEL=OFF \
+        -DBUILD_PYTHON=ON \
+        -DBUILD_PYCALL_PLUGIN=ON \
+        -DBUILD_NETCDF_PARALLEL=OFF \
+        -DCMAKE_INSTALL_PREFIX=/usr/local \
+        .. && \
+    make -j$(nproc) && \
+    make install && \
+    ldconfig && \
+    cd / && rm -rf /tmp/pdi-build
+
+# -----------------------------------------------------------------------------
+# 4. USER CONFIGURATION & RUNTIME ENVIRONMENT
+# -----------------------------------------------------------------------------
+RUN groupadd -g ${GROUP_ID} ${USER_NAME} && \
+    useradd -m -u ${USER_ID} -g ${USER_NAME} -s /bin/bash ${USER_NAME} && \
+    echo "${USER_NAME} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+
+# RUNTIME ENVIRONMENT VARIABLES - CRITICAL SETTINGS
+# 1. LD_LIBRARY_PATH: STRICTLY excludes '/usr/lib/x86_64-linux-gnu'.
+#    Reason: Preventing "DLL Hell". Including system paths forces Julia to load system
+#    libraries (e.g., system libglib) instead of its own Artifacts, causing undefined
+#    symbol errors (e.g., 'g_string_copy'). We prioritize Julia and PDI libs.
+ENV LD_LIBRARY_PATH=/usr/local/julia/lib:/usr/local/julia/lib/julia:/usr/local/lib
+
+# 2. GTK_A11Y=none: Disables GTK Accessibility Bus to suppress "org.a11y.Bus" warnings in logs.
+ENV GTK_A11Y=none
+
+# 3. Graphics & Julia settings
+ENV GKSwstype=100
+ENV JULIA_PKG_PRECOMPILE_AUTO=0
+ENV JULIA_PKG_USE_CLI_GIT=true
+ENV DISPLAY=host.docker.internal:0.0
+ENV PYTHONPATH=/usr/local/lib/python3/dist-packages
+
+# Switch to non-root user for Package Installation
+# Ensures ~/.julia permissions are correctly set for the user 'coder'.
+USER ${USER_NAME}
+WORKDIR /home/${USER_NAME}/project
+
+# -----------------------------------------------------------------------------
+# 5. JULIA PACKAGES INSTALLATION
+# -----------------------------------------------------------------------------
+# Optimization:
+# - Operations are consolidated into a single RUN instruction to reduce Docker layer count.
+# - xvfb-run: Executes in a virtual framebuffer. Essential for 'Pkg.precompile()'
+#   of Gtk4 and ProfileView, which require a display server even during installation.
+
+
+
+
+ENV LD_LIBRARY_PATH=/usr/local/julia/lib:/usr/local/julia/lib/julia:/usr/local/lib
+
+RUN julia -e 'import Pkg; \
+    Pkg.add([ \
+		"Pkg", \
+        "AbstractTrees", \
+		"BenchmarkTools", \ 
+		"Cairo_jll", \
+		"Documenter", \ 
+		"GeoInterface", \
+		"GeometryBasics", \ 
+		"HDF5", \ 
+		"Interpolations", \ 
+		"IterativeSolvers", \ 
+		"JLD", \ 
+		"LibGEOS", \ 
+		"LinearAlgebra", \ 
+		"LsqFit", \ 
+		"MPI", \ 
+		"MUMPS", \
+		"MethodAnalysis", \ 
+		"OffsetArrays", \ 
+		"PProf", \
+		"PackageCompiler", \ 
+		"Parameters", \ 
+		"Peaks", \
+		"Polynomials", \
+		"Printf", \ 
+		"Profile", \ 
+		"PropertyDicts", \
+		"Revise", \ 
+		"Roots", \ 
+		"SnoopCompileCore", \
+		"SparseArrays", \ 
+		"SpecialFunctions", \
+		"StaticArrays", \
+		"Statistics", \ 
+		"Test", \
+		"YAML" \
+	])'
+RUN xvfb-run --auto-servernum --server-args="-screen 0 1920x1080x24 -nolisten tcp" \
+	julia -e 'import Pkg; \
+       Pkg.add([ \		
+        "DataFrames", \
+        "Gtk4", \
+        "Gtk", \
+        "ProfileView", \
+        "PProf", \
+        "Reexport" \
+    ])'
+
+
+ENV LD_LIBRARY_PATH=""
+# hack to install julia package
+RUN xvfb-run --auto-servernum --server-args="-screen 0 1920x1080x24 -nolisten tcp" \
+    julia -e 'import Pkg; Pkg.precompile()'
+RUN xvfb-run --auto-servernum --server-args="-screen 0 1920x1080x24 -nolisten tcp" \
+    julia -e 'import Pkg; Pkg.update(); Pkg.precompile()'
+ENV LD_LIBRARY_PATH=/usr/local/julia/lib:/usr/local/julia/lib/julia:/usr/local/lib
+
+
+
+CMD ["/bin/bash"]