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Added a Dockerfile to build a conda environment with py-mochi-sonata installed, giving users a clean python environment free from spack
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‎docker/ubuntu18.04/openmpi4.0.4/conda_sonata/Dockerfile‎

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FROM ubuntu:18.04 as base
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SHELL ["/bin/bash", "-c"]
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RUN mkdir -p /Downloads
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update && \
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apt-get install -y tzdata && \
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ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime && \
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dpkg-reconfigure --frontend noninteractive tzdata && \
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apt-get install -y build-essential wget git-core libtool libtool-bin \
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python3 python3-dev \
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curl psmisc iproute2 gfortran libssl-dev locales && \
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apt autoremove -y && \
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rm -rf /var/lib/apt/lists/* && \
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locale-gen en_US.UTF-8 && dpkg-reconfigure locales
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ENV LANG en_US.UTF-8
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ENV LANGUAGE en_US:en
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ENV LC_ALL en_US.UTF-8
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from base as build
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RUN mkdir /spack && cd /spack && git clone https://github.com/spack/spack.git -b v0.23.1 --single-branch
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RUN mkdir /sds && cd /sds && git clone https://github.com/mochi-hpc/mochi-spack-packages.git && cd mochi-spack-packages && git checkout 29a196f299130ff8039bdfdc9b22715f7e6991dc
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RUN mkdir -p /opt/spack-environment
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RUN echo "RESET 3" >> /dev/null
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COPY env.yaml /opt/spack-environment/spack.yaml
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#apparently spack needs unzip!
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RUN apt-get update && apt-get install unzip
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RUN source /spack/spack/share/spack/setup-env.sh && cd /opt/spack-environment && spack env activate . && spack concretize -f && spack install && spack gc -y && spack clean -a
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COPY modules.yaml /root/.spack
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#install conda environment with py-mochi services
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RUN cd /opt/spack-environment/ && \
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source /spack/spack/share/spack/setup-env.sh && \
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spack env activate . && \
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spack load pkgconf && \
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cd /Downloads/ && \
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
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chmod u+x Miniconda3-latest-Linux-x86_64.sh && \
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./Miniconda3-latest-Linux-x86_64.sh -p /conda -b && \
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source /conda/bin/activate && \
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conda create -n "conda-env" python=3.8.0 -y && \
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conda activate conda-env && \
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pip install wheel pybind11 pkgconfig && \
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git clone https://github.com/mochi-hpc/py-mochi-margo.git && \
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cd py-mochi-margo/ && \
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git checkout 976b14982f02bc98eac1b32052de5e8ec69fa081 && \
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python setup.py bdist_wheel && \
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pip install dist/pymargo-0.5.1-cp38-cp38-linux_x86_64.whl && \
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cd .. && \
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git clone https://github.com/mochi-hpc/py-mochi-sonata.git && \
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cd py-mochi-sonata/ && \
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git checkout 21ff608c81419470a26de645be5dad5d4aa35653 && \
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python setup.py bdist_wheel && \
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pip install dist/py_sonata-0.1-cp38-cp38-linux_x86_64.whl && \
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rm -rf /Downloads/*
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#ensure shared libraries visible
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ENV LD_LIBRARY_PATH /opt/view/lib/
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#python is now freed from the tyranny of spack!
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#install provdb-python
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RUN source /conda/bin/activate && \
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conda activate conda-env && \
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cd /Downloads && \
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git clone https://github.com/CODARcode/PerformanceAnalysis.git && \
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cd PerformanceAnalysis/ && \
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git checkout 6be55788fcc962a0bbb4ae9191404328afcfbe90 && \
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cd scripts/provdb_python && \
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python setup.py bdist_wheel && \
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pip install dist/provdb_python-0.0.1-py3-none-any.whl && \
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rm -rf /Downloads/*
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ENTRYPOINT ["/bin/bash"]

‎docker/ubuntu18.04/openmpi4.0.4/conda_sonata/docker_rebuild_stack.sh‎

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#!/bin/bash
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set -e
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docker build --progress=plain -f Dockerfile -t chimbuko/chimbuko-conda:ubuntu18.04 .

‎docker/ubuntu18.04/openmpi4.0.4/conda_sonata/env.yaml‎

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spack:
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specs:
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- mochi-sonata~bedrock~unqlite_st
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concretizer:
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unify: true
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compilers:
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- compiler:
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spec: gcc@=7.5.0
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paths:
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cc: /usr/bin/gcc
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cxx: /usr/bin/g++
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f77: /usr/bin/gfortran
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fc: /usr/bin/gfortran
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flags: {}
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operating_system: ubuntu18.04
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target: x86_64
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modules: []
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environment: {}
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extra_rpaths: []
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repos:
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- /sds/mochi-spack-packages
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packages:
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all:
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compiler: [gcc@=7.5.0]
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providers: {}
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coreutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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diffutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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findutils:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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openssh:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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openssl:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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git:
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externals:
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- spec: [email protected]~tcltk
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prefix: /usr
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buildable: False
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gmake:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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libtool:
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externals:
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- spec: [email protected]
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prefix: /usr
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buildable: False
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config:
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install_tree: /opt/software
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view: /opt/view

‎docker/ubuntu18.04/openmpi4.0.4/conda_sonata/modules.yaml‎

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modules:
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prefix_inspections:
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lib: [LIBRARY_PATH]
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lib64: [LIBRARY_PATH]
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include:
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- C_INCLUDE_PATH
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- CPLUS_INCLUDE_PATH
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- INCLUDE

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