mirror of
https://github.com/JHUAPL/kaiju.git
synced 2026-01-08 02:23:51 -05:00
86d1e1876e
This includes a Docker definitoin file for AWS (Dockerfile) and a singularity definition file (gamera.def) for NASA NAS.
100 lines
3.9 KiB
Docker
100 lines
3.9 KiB
Docker
#==============================================================================
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# CGS GAMERA (Serial) Containerization
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#
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# This Dockerfile allows one to create a build environment for the GAMERA model.
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# The base image/layer is Intel's OneAPI HPC Toolkit allowing for Intel-based
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# compilers.
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#
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# Run:
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# docker build -t <image_tag> . && docker run --rm -it <image_tag>
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#
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# Note: The initial build will take longer as Docker will be retrieving the
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# base image (~5.5GB). This time will vary depending upon your network.
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# Note: The base image may fail to build (known issue). If it does, that
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# means that Intel's container repository is having network issues.
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# A work-around is in development.
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#
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# 2024, Brent Smith
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#==============================================================================
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FROM intel/oneapi-hpckit:2023.2.1-devel-ubuntu22.04
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# Intel OneAPI Docker Images:
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# https://github.com/intel/oneapi-containers/tree/master/images
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# https://hub.docker.com/r/intel/oneapi-hpckit
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# Directory Structure
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RUN mkdir -p /cdf /hdf5 /miniconda3 /kaiju
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#------------------------------------------------------------------------------
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# NASA CDF Library (version 3.9.0)
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ENV CDF_FILE=cdf39_0-dist-all.tar.gz
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ADD https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/cdf39_0/linux/${CDF_FILE} /cdf/${CDF_FILE}
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RUN cd /cdf && tar xf ${CDF_FILE} && cd cdf39_0-dist &&\
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make OS=linux ENV=gnu CURSES=no all &&\
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make INSTALLDIR=/cdf install &&\
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rm ../${CDF_FILE} &&\
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. /cdf/bin/definitions.B
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# HDF5 Library
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ENV HDF_FILE=hdf5-1.14.1-2
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ADD https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.1/src/${HDF_FILE}.tar.gz /hdf5/${HDF_FILE}.tar.gz
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RUN cd /hdf5 && tar zxf ${HDF_FILE}.tar.gz && cd ${HDF_FILE} &&\
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./configure FC=ifort --prefix=/hdf5 --enable-fortran &&\
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make && make install &&\
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rm ../${HDF_FILE}.tar.gz
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ENV PATH="/hdf5/bin:${PATH}" \
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HDF5_DIR=/hdf5 \
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HDF5_INCLUDE_DIRS=/hdf5/include \
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HDF5_LIBRARIES=/hdf5/lib \
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CPATH=${HDF5_INCLUDE_DIRS} \
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INCLUDE="-I${HDF5_INCLUDE_DIRS}" \
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LD_LIBRARY_PATH="/hdf5:${LD_LIBRARY_PATH}"
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# Update System
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# known GPG key issue: https://github.com/intel/oneapi-containers/issues/53
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RUN curl -fsSL https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | gpg --dearmor > /usr/share/keyrings/intel-oneapi-archive-keyring.gpg
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RUN apt -y update && \
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apt install --no-install-recommends -y \
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build-essential \
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cmake \
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git \
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git-lfs \
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libgeos-dev \
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pkg-config && \
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# vim \
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rm -rf /var/lib/apt/lists/*
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# Python Environment
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ENV PY_FILE=Miniconda3-latest-Linux-x86_64.sh
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COPY requirements.txt /miniconda3/
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ADD https://repo.anaconda.com/miniconda/${PY_FILE} /miniconda3/${PY_FILE}
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RUN cd /miniconda3 && bash ${PY_FILE} -b -u -p /miniconda3 && \
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rm ${PY_FILE} && /miniconda3/bin/conda init bash && \
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. ~/.bashrc && \
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conda config --set ssl_verify false && \
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conda config --set auto_activate_base false && \
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conda update -y --all && \
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conda create -n kaiju-3.8 python=3.8 -y && \
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conda activate kaiju-3.8 && \
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conda update -y --all && \
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pip3 install --default-timeout=100 -r /miniconda3/requirements.txt
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#==============================================================================
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# CGS GAMERA Setup/Compilation
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ENV KAIJUHOME=/kaiju \
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FC=/hdf5/bin/h5fc
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# Build pre-cloned repository code on user-defined branch (development)
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COPY . /kaiju/
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RUN cd /kaiju/ && git remote rm origin && \
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mkdir -p ${KAIJUHOME}/build && cd ${KAIJUHOME}/build && \
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cmake -DALLOW_INVALID_COMPILERS=ON .. && \
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make all
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# Setup Running ENV and entry directory
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WORKDIR /kaiju/build/
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ENV PATH=${KAIJUHOME}/quickstart/loop2d:${PATH}
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RUN echo "conda activate kaiju-3.8" >> ~/.bashrc && \
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echo ". /cdf/bin/definitions.B" >> ~/.bashrc && \
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echo ". \${KAIJUHOME}/scripts/setupEnvironment.sh" >> ~/.bashrc && \
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echo "PATH=\${KAIJUHOME}/build/bin:\${PATH}" >> ~/.bashrc |