Merge branch 'rnou/351-preparing-new-docker-for-0-9-5' into 'master' (6ad9195b) · Commits · hpc / gekkofs

CMake/load_nlohmann_json.cmake

+1 −7

Original line number	Diff line number	Diff line
		@@ -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 ()

docker/0.9.5/apps/Dockerfile

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		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

docker/0.9.5/apps/Makefile

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		.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 .

docker/0.9.5/apps/sources.json

0 → 100644

+27 −0

Original line number	Diff line number	Diff line
		{
		"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

docker/0.9.5/apps/wacomm.json

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		{
		"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