From bc59a45c9d0bddc922dfbbab6fd923a17730219e Mon Sep 17 00:00:00 2001
From: Ramon Nou <ramon.nou@bsc.es>
Date: Mon, 12 May 2025 07:41:15 +0200
Subject: [PATCH] DockerFiles updated for 0.9.5

---
 CMake/load_nlohmann_json.cmake  |  8 +---
 docker/0.9.5/apps/Dockerfile    | 72 +++++++++++++++++++++++++++++++++
 docker/0.9.5/apps/Makefile      | 10 +++++
 docker/0.9.5/apps/sources.json  | 27 +++++++++++++
 docker/0.9.5/apps/wacomm.json   | 46 +++++++++++++++++++++
 docker/0.9.5/core/Dockerfile    | 35 ++++++++++++++++
 docker/0.9.5/core/Makefile      | 10 +++++
 docker/0.9.5/deps/Dockerfile    | 37 +++++++++++++++++
 docker/0.9.5/deps/Makefile      | 23 +++++++++++
 docker/0.9.5/docs/Dockerfile    | 25 ++++++++++++
 docker/0.9.5/docs/Makefile      | 10 +++++
 docker/0.9.5/linter/Dockerfile  | 14 +++++++
 docker/0.9.5/linter/Makefile    | 10 +++++
 docker/0.9.5/testing/Dockerfile | 54 +++++++++++++++++++++++++
 docker/0.9.5/testing/Makefile   | 10 +++++
 docker/latest                   |  2 +-
 tests/unit/CMakeLists.txt       | 10 +----
 17 files changed, 386 insertions(+), 17 deletions(-)
 create mode 100644 docker/0.9.5/apps/Dockerfile
 create mode 100644 docker/0.9.5/apps/Makefile
 create mode 100644 docker/0.9.5/apps/sources.json
 create mode 100644 docker/0.9.5/apps/wacomm.json
 create mode 100644 docker/0.9.5/core/Dockerfile
 create mode 100644 docker/0.9.5/core/Makefile
 create mode 100644 docker/0.9.5/deps/Dockerfile
 create mode 100644 docker/0.9.5/deps/Makefile
 create mode 100644 docker/0.9.5/docs/Dockerfile
 create mode 100644 docker/0.9.5/docs/Makefile
 create mode 100644 docker/0.9.5/linter/Dockerfile
 create mode 100644 docker/0.9.5/linter/Makefile
 create mode 100644 docker/0.9.5/testing/Dockerfile
 create mode 100644 docker/0.9.5/testing/Makefile

diff --git a/CMake/load_nlohmann_json.cmake b/CMake/load_nlohmann_json.cmake
index 34a5f4633..cb059db79 100644
--- a/CMake/load_nlohmann_json.cmake
+++ b/CMake/load_nlohmann_json.cmake
@@ -34,12 +34,8 @@ FetchContent_Declare(nlohmann_json
     DOWNLOAD_EXTRACT_TIMESTAMP ON
     URL https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz)
 
-FetchContent_GetProperties(nlohmann_json)
 
-if (NOT nlohmann_json_POPULATED)
-    FetchContent_Populate(nlohmann_json)
-    message(STATUS "[gkfs.io] Nlohmann JSON source dir: ${nlohmann_json_SOURCE_DIR}")
-    message(STATUS "[gkfs.io] Nlohmann JSON binary dir: ${nlohmann_json_BINARY_DIR}")
+FetchContent_MakeAvailable(nlohmann_json)
 
     # we don't really care so much about a third party library's tests to be
     # run from our own project's code
@@ -48,5 +44,3 @@ if (NOT nlohmann_json_POPULATED)
     # we also don't need to install it when our main project gets installed
     set(JSON_Install OFF CACHE INTERNAL "")
 
-    add_subdirectory(${nlohmann_json_SOURCE_DIR} ${nlohmann_json_BINARY_DIR})
-endif ()
diff --git a/docker/0.9.5/apps/Dockerfile b/docker/0.9.5/apps/Dockerfile
new file mode 100644
index 000000000..89317fa97
--- /dev/null
+++ b/docker/0.9.5/apps/Dockerfile
@@ -0,0 +1,72 @@
+FROM gekkofs/testing:0.9.5 AS builder
+
+LABEL Description="Build environment for S3D-IO and WaComM++"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN <<EOF
+    apt-get update
+    apt-get install -y --no-install-recommends \
+    openmpi-bin openmpi-common gfortran libopenmpi-dev pnetcdf-bin libpnetcdf-dev libssl-dev wget nco nghttp2
+    rm -rf /var/lib/apt/lists/* 
+    apt-get clean
+    apt-get autoclean
+EOF
+
+# --- Build S3D-IO ---
+WORKDIR /build/S3D-IO
+RUN git clone https://github.com/wkliao/S3D-IO.git . && \
+    # Note: The PNETCDF_DIR and include path might need adjustment if libpnetcdf-dev installs to a different standard location
+    # or if the base image structure changes.
+    sed -i -e 's/PNETCDF_DIR = ${HOME}\/PNetCDF/PNETCDF_DIR = \/usr/' \
+            -e 's/\(INC[[:space:]]*=[[:space:]]*-I\$(PNETCDF_DIR)\/include\)/\1 -I\/usr\/lib\/x86_64-linux-gnu\/fortran\/gfortran-mod-15/' Makefile && \
+    make && \
+    mv s3d_io.x /usr/local/bin/s3d_io.x
+
+# --- Build wacommplusplus ---
+WORKDIR /build/wacommplusplus
+RUN git clone https://github.com/CCMMMA/wacommplusplus.git . && \
+    sed -i 's|\${LIBCURL}|/usr/lib/x86_64-linux-gnu/libcurl.so|g' CMakeLists.txt && \
+    mkdir build && cd build && \
+    cmake .. && \
+    make -j$(nproc) && \
+    mv wacommplusplus /usr/local/bin/wacommplusplus && \
+    mv external /usr/local/lib/
+
+# ---- Final Stage ----
+FROM gekkofs/testing:0.9.5
+
+LABEL Description="Debian-based environment to test GekkoFS with apps"
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install runtime dependencies
+# libpnetcdf13 (or similar, check exact name with 'apt-cache search libpnetcdf')
+# libssl might be libssl1.1 or libssl3 depending on Debian version in base image
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    openmpi-bin openmpi-common libopenmpi-dev pnetcdf-bin libssl3 libcurl4 \
+    wget nco nghttp2 \
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get clean && \
+    mkdir -p /root/wacommplusplus/build/example /root/S3D-IO
+
+# Copy built applications from the builder stage
+COPY --from=builder /usr/local/bin/s3d_io.x /root/S3D-IO
+COPY --from=builder /usr/local/bin/wacommplusplus /root/wacommplusplus/build
+COPY --from=builder /usr/local/lib/external /root/wacommplusplus/build/external/
+
+
+WORKDIR /root/wacommplusplus/build/example
+RUN mkdir -p input processed output restarts && \
+    cd input && \
+    wget -q https://api.meteo.uniparthenope.it/files/rms3/d03/history/2025/01/01/rms3_d03_20250101Z0000.nc && \
+    mv rms3_d03_20250101Z0000.nc input.nc && \
+    ncks -7 -L 9 --qnt default=1 --ppc default=1 input.nc rms3_d03_20250101Z0000.nc && \
+    tar cvzf rms.tar.gz rms3_d03_20250101Z0000.nc && \
+    rm rms3_d03_20250101Z0000.nc input.nc
+
+# Copy configuration files
+# These files (sources.json, wacomm.json) should be in the same directory as your Dockerfile
+COPY sources.json /root/wacommplusplus/build/example
+COPY wacomm.json /root/wacommplusplus/build/example
+
+ENV LD_LIBRARY_PATH=/root/wacommplusplus/build/external/lib/
\ No newline at end of file
diff --git a/docker/0.9.5/apps/Makefile b/docker/0.9.5/apps/Makefile
new file mode 100644
index 000000000..c189defdf
--- /dev/null
+++ b/docker/0.9.5/apps/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all
+
+amd64:
+	docker build --platform amd64 -t gekkofs/apps:0.9.5 .
+
+aarch64:
+	docker build --platform aarch64 -t gekkofs/apps:0.9.5 .
+
+all:
+	docker build -t gekkofs/apps:0.9.5 .
diff --git a/docker/0.9.5/apps/sources.json b/docker/0.9.5/apps/sources.json
new file mode 100644
index 000000000..ead4beb58
--- /dev/null
+++ b/docker/0.9.5/apps/sources.json
@@ -0,0 +1,27 @@
+{
+    "type": "FeatureCollection",
+    "crs": {
+        "type": "name",
+        "properties": {
+            "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+        }
+    },
+    "features": [
+        {
+            "type": "Feature",
+            "properties": {
+                "start": -1.0,
+                "end": -1.0,
+                "mode": 1,
+                "particlesPerHour": 100,
+                "depth": 0.0,
+                "id": "1"
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    14.972061,
+                    40.343286
+                ]
+            }
+        } ] }
\ No newline at end of file
diff --git a/docker/0.9.5/apps/wacomm.json b/docker/0.9.5/apps/wacomm.json
new file mode 100644
index 000000000..145224094
--- /dev/null
+++ b/docker/0.9.5/apps/wacomm.json
@@ -0,0 +1,46 @@
+{
+    "io": {
+    "base_path": "/root/wacommplusplus/build/example/input",
+    "history_root": "/root/wacommplusplus/build/example/restarts/",
+    "mask_output": true,
+    "nc_input_root": "/root/wacommplusplus/build/example/input/rms3_d03",
+    "nc_inputs": [
+                    "rms3_d03_20250101Z0000.nc"
+            ],
+    "nc_output_root": "/root/wacommplusplus/build/example/output/wacomm_his_",
+    "ocean_model": "ROMS",
+    "save_history": "json",
+    "save_input": false,
+    "timestep": 3600
+},
+"physics": {
+    "horizontal_closure": "kill",
+    "lower_closure": "kill",
+    "random": true,
+    "random_sources": true,
+    "shore_limit": 0.5,
+    "sigma": 3.46,
+    "survprob": 0.0001,
+    "sv": 0,
+    "tau0": 86400.0,
+    "upper_closure": "reflection"
+},
+"restart": {
+    "active": false,
+    "interval": 3600,
+    "restart_file": ""
+},
+"simulation": {
+    "dry": false,
+    "end": "20250101Z00",
+    "hours": 24,
+    "institution": "meteo@uniparthenope - Department of Science and Technologies, University of Naples Parthenope",
+    "name": "WaComM++",
+    "start": "20250101Z01",
+    "url": "https://meteo.uniparthenope.it"
+},
+"sources": {
+    "active": true,
+    "sources_file": "sources.json" 
+}
+}
\ No newline at end of file
diff --git a/docker/0.9.5/core/Dockerfile b/docker/0.9.5/core/Dockerfile
new file mode 100644
index 000000000..4895c9cf9
--- /dev/null
+++ b/docker/0.9.5/core/Dockerfile
@@ -0,0 +1,35 @@
+FROM debian:trixie-slim
+
+LABEL Description="Debian-based environment suitable to build GekkoFS and its dependencies"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+		git \
+		curl \
+		ca-certificates \
+		libtool \
+		pkg-config \
+		make \
+		automake \
+		gcc \
+		g++ \
+		ninja-build \
+		procps \
+		# AGIOS dependencies
+		libconfig-dev \
+		# Mercury dependencies
+		libltdl-dev \
+		lbzip2 \
+        # Margo dependencies \
+        libjson-c-dev \
+		# RocksDB dependencies
+		liblz4-dev \
+		# syscall_intercept dependencies
+		# libcapstone-dev \
+		# GekkoFS dependencies
+		libboost-program-options-dev \
+		uuid-dev ccache cmake && \
+    # Clean apt cache to reduce image layer size
+    rm -rf /var/lib/apt/lists/* && \
+    # Clean apt caches of packages
+    apt-get clean && apt-get autoclean 
diff --git a/docker/0.9.5/core/Makefile b/docker/0.9.5/core/Makefile
new file mode 100644
index 000000000..293d01099
--- /dev/null
+++ b/docker/0.9.5/core/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all
+
+amd64:
+	docker buildx build --platform amd64 -t gekkofs/core:0.9.5 .
+
+aarch64:
+	docker buildx build --platform aarch64 -t gekkofs/core:0.9.5 .
+
+all:
+	docker buildx build -t gekkofs/core:0.9.5 .
diff --git a/docker/0.9.5/deps/Dockerfile b/docker/0.9.5/deps/Dockerfile
new file mode 100644
index 000000000..b258fa9c8
--- /dev/null
+++ b/docker/0.9.5/deps/Dockerfile
@@ -0,0 +1,37 @@
+FROM gekkofs/core:0.9.5
+
+LABEL Description="Debian-based environment to build GekkoFS"
+
+ENV GKFS_PATH=/opt/gkfs
+ENV GKFS_VERSION=0.9.5
+
+ENV SCRIPTS_PATH=${GKFS_PATH}/scripts
+ENV DEPS_SRC_PATH=${GKFS_PATH}/deps_src
+ENV INSTALL_PATH=/usr/local
+
+COPY scripts/dl_dep.sh		${SCRIPTS_PATH}/
+COPY scripts/compile_dep.sh ${SCRIPTS_PATH}/
+COPY scripts/patches        ${SCRIPTS_PATH}/patches
+COPY scripts/profiles       ${SCRIPTS_PATH}/profiles
+
+RUN apt-get update && \
+  apt-get install -y --no-install-recommends \
+  python3 \
+  python3-pip \
+  python3-dev \
+  python3-venv \
+  python3-setuptools \
+  libnuma-dev libyaml-dev libcurl4-openssl-dev \
+  procps && \
+  rm -rf /var/lib/apt/lists/* && \
+  apt-get clean && apt-get autoclean
+
+# Download and build dependencies
+RUN cd ${SCRIPTS_PATH} && \
+  /bin/bash ./dl_dep.sh -p ci:${GKFS_VERSION} ${DEPS_SRC_PATH} && \
+  /bin/bash ./compile_dep.sh -j 8 -p ci:${GKFS_VERSION} ${DEPS_SRC_PATH} ${INSTALL_PATH} && \
+  cp ${DEPS_SRC_PATH}/parallax/lib/include/parallax/structures.h ${INSTALL_PATH}/include/ &&\
+  rm -rf ${DEPS_SRC_PATH} && \
+  rm -rf ${SCRIPTS_PATH} && \
+  rmdir ${GKFS_PATH} && \
+  ldconfig
diff --git a/docker/0.9.5/deps/Makefile b/docker/0.9.5/deps/Makefile
new file mode 100644
index 000000000..1dc11d6b7
--- /dev/null
+++ b/docker/0.9.5/deps/Makefile
@@ -0,0 +1,23 @@
+CWD:=$(shell pwd)
+GIT_ROOT:=$(shell git rev-parse --show-toplevel)
+
+.PHONY: all build copy-scripts remove-scripts
+
+all: build copy-scripts remove-scripts
+amd64: build-amd64 copy-scripts remove-scripts
+aarch64: build-aarch64 copy-scripts remove-scripts
+
+copy-scripts:
+	cp -R $(GIT_ROOT)/scripts $(CWD)/scripts
+
+build: copy-scripts
+	docker build -t gekkofs/deps:0.9.5 .
+
+build-amd64: copy-scripts
+	docker build --platform amd64 -t gekkofs/deps:0.9.5 .
+
+build-aarch64: copy-scripts
+	docker build --platform aarch64 -t gekkofs/deps:0.9.5 .
+
+remove-scripts:
+	- rm -rf $(CWD)/scripts
diff --git a/docker/0.9.5/docs/Dockerfile b/docker/0.9.5/docs/Dockerfile
new file mode 100644
index 000000000..ab5781a7e
--- /dev/null
+++ b/docker/0.9.5/docs/Dockerfile
@@ -0,0 +1,25 @@
+FROM gekkofs/deps:0.9.5
+
+LABEL Description="Debian-based environment suitable to build GekkoFS' documentation"
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    # install dependencies for Doxygen
+    python3 \
+    flex \
+    bison \
+    graphviz doxygen && \
+    # install sphinx, breathe and exhale
+    pip3 install --break-system-packages \
+    'sphinx' \
+    sphinx_rtd_theme \
+    'breathe' \
+    'exhale' \
+    'sphinx-copybutton' \
+    'sphinx-multiversion' \
+    'myst_parser'  \
+    attrs && \
+    # Clean apt cache to reduce image layer size
+    rm -rf /var/lib/apt/lists/* && \
+    # Clean apt caches of packages
+    apt-get clean && apt-get autoclean
diff --git a/docker/0.9.5/docs/Makefile b/docker/0.9.5/docs/Makefile
new file mode 100644
index 000000000..3d3fe42dd
--- /dev/null
+++ b/docker/0.9.5/docs/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all
+
+amd64:
+	docker build --platform amd64 -t gekkofs/docs:0.9.5 .
+
+aarch64:
+	docker build --platform aarch64 -t gekkofs/docs:0.9.5 .
+
+all:
+	docker build -t gekkofs/docs:0.9.5 .
diff --git a/docker/0.9.5/linter/Dockerfile b/docker/0.9.5/linter/Dockerfile
new file mode 100644
index 000000000..6253c8fc1
--- /dev/null
+++ b/docker/0.9.5/linter/Dockerfile
@@ -0,0 +1,14 @@
+FROM gekkofs/core:0.9.5
+
+LABEL Description="Debian-based environment to check the formatting of GekkoFS code"
+
+RUN apt-get update && \
+  apt-get install -y --no-install-recommends \
+  # clang 15 deps for clang-format
+  lsb-release \
+  wget \
+  gnupg2 \
+  clang-format && \
+  rm -rf /var/lib/apt/lists/* && \
+  # Clean apt caches of packages
+  apt-get clean && apt-get autoclean
diff --git a/docker/0.9.5/linter/Makefile b/docker/0.9.5/linter/Makefile
new file mode 100644
index 000000000..4d19d9eaa
--- /dev/null
+++ b/docker/0.9.5/linter/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all
+
+amd64:
+	docker buildx build --platform amd64 -t gekkofs/linter:0.9.5 .
+
+aarch64:
+	docker buildx build --platform aarch64 -t gekkofs/linter:0.9.5 .
+
+all:
+	docker buildx build -t gekkofs/linter:0.9.5 .
diff --git a/docker/0.9.5/testing/Dockerfile b/docker/0.9.5/testing/Dockerfile
new file mode 100644
index 000000000..77a2f2172
--- /dev/null
+++ b/docker/0.9.5/testing/Dockerfile
@@ -0,0 +1,54 @@
+FROM gekkofs/deps:0.9.5
+
+LABEL Description="Debian-based environment to test GekkoFS with LCOV, cppcheck, and reporting tools"
+
+# Set DEBIAN_FRONTEND to noninteractive to prevent apt-get from prompting
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    # LCOV's genhtml dependencies
+    libgd-perl \
+    libcapture-tiny-perl \
+    libdatetime-perl \
+    libtimedate-perl \
+    libjson-xs-perl \
+    # Other system tools
+    binutils \
+    cppcheck \
+    curl \
+    git \
+    make \
+    # Python3 and pip are assumed to be in gekkofs/deps:0.9.5
+    # If not, add python3 python3-pip
+    && \
+    # Cleanup apt cache
+    rm -rf /var/lib/apt/lists/* && \
+    apt-get clean
+
+# Install Python packages
+RUN pip3 install --no-cache-dir --break-system-packages \
+    loguru \
+    lcov_cobertura
+
+# Install LCOV from source
+WORKDIR /tmp
+RUN LCOV_VERSION="2.3.1" && \
+    curl -sSOL "https://github.com/linux-test-project/lcov/releases/download/v${LCOV_VERSION}/lcov-${LCOV_VERSION}.tar.gz" && \
+    tar xfz "lcov-${LCOV_VERSION}.tar.gz" && \
+    cd "lcov-${LCOV_VERSION}" && \
+    make install && \
+    cd .. && \
+    rm -rf "lcov-${LCOV_VERSION}.tar.gz" "lcov-${LCOV_VERSION}"
+
+WORKDIR /opt
+RUN git clone https://gitlab.com/ahogen/cppcheck-codequality.git && \
+    cd cppcheck-codequality && \
+    git checkout 61f6ae3b150d377e9987dce9d1c2859ef08bea6f && \
+    sed -i 's/python = ">=3\.7,<3\.13"/python = ">=3.7,<3.14"/' pyproject.toml && \
+    sed -i 's/python = ">=3\.7,<3\.13"/python = ">=3.7,<3.14"/' poetry.lock && \
+    pip3 install --no-cache-dir --break-system-packages . && \
+    cd .. && \
+    rm -rf cppcheck-codequality
+
+WORKDIR /
\ No newline at end of file
diff --git a/docker/0.9.5/testing/Makefile b/docker/0.9.5/testing/Makefile
new file mode 100644
index 000000000..f55598994
--- /dev/null
+++ b/docker/0.9.5/testing/Makefile
@@ -0,0 +1,10 @@
+.PHONY: all
+
+amd64:
+	docker build --platform amd64 -t gekkofs/testing:0.9.5 .
+
+aarch64:
+	docker build --platform aarch64 -t gekkofs/testing:0.9.5 .
+
+all:
+	docker build -t gekkofs/testing:0.9.5 .
diff --git a/docker/latest b/docker/latest
index 2bd77c74f..03834411d 120000
--- a/docker/latest
+++ b/docker/latest
@@ -1 +1 @@
-0.9.4
\ No newline at end of file
+0.9.5
\ No newline at end of file
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 72e2d63d2..004671439 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -37,15 +37,7 @@ FetchContent_Declare(catch2
     GIT_PROGRESS ON
 )
 
-FetchContent_GetProperties(catch2)
-
-if (NOT catch2_POPULATED)
-    FetchContent_Populate(catch2)
-    message(STATUS "[gkfs] Catch2 source dir: ${catch2_SOURCE_DIR}")
-    message(STATUS "[gkfs] Catch2 binary dir: ${catch2_BINARY_DIR}")
-    set(CATCH_BUILD_TESTING OFF CACHE INTERNAL "")
-    add_subdirectory(${catch2_SOURCE_DIR} ${catch2_BINARY_DIR})
-endif ()
+FetchContent_MakeAvailable(catch2)
 
 add_subdirectory(helpers)
 
-- 
GitLab