MR1: Update dependency scripts to 0.9.6

FROM gekkofs/testing:0.9.6 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:0.9.6

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

COPY rms.tar.gz /root/wacommplusplus/build/example/input/

RUN mkdir -p input processed output restarts && \

    cd input && \

    tar xzf rms.tar.gz && \

    rm rms.tar.gz

# 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/

.PHONY: all

amd64:

	docker build --platform amd64 -t gekkofs/apps:0.9.6 .

aarch64:

	docker build --platform aarch64 -t gekkofs/apps:0.9.6 .

all:

	docker build -t gekkofs/apps:0.9.6 .

{

    "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

                ]

            }

        } ] }

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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" 

}

}

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