matthias muntwiler
acea809e4e
based on internal repository c9a2ac8 2019-01-03 16:04:57 +0100 tagged rev-master-2.0.0
118 lines
2.6 KiB
Plaintext
118 lines
2.6 KiB
Plaintext
BootStrap: debootstrap
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OSVersion: bionic
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MirrorURL: http://ch.archive.ubuntu.com/ubuntu/
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%help
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a singularity container for PMSCO.
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git clone requires an ssh key for git.psi.ch.
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try agent forwarding (-A option to ssh).
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#%setup
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# executed on the host system outside of the container before %post
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#
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# this will be inside the container
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# touch ${SINGULARITY_ROOTFS}/tacos.txt
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# this will be on the host
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# touch avocados.txt
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#%files
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# files are copied before %post
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#
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# this copies to root
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# avocados.txt
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# this copies to /opt
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# avocados.txt /opt
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#
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# this does not work
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# ~/.ssh/known_hosts /etc/ssh/ssh_known_hosts
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# ~/.ssh/id_rsa /etc/ssh/id_rsa
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%labels
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Maintainer Matthias Muntwiler
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Maintainer_Email matthias.muntwiler@psi.ch
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Python_Version 3
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%environment
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export PATH="/usr/local/miniconda3/bin:$PATH"
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export PYTHON_VERSION=3
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export SINGULAR_BRANCH="singular"
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export LC_ALL=C
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%post
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export PYTHON_VERSION=3
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export LC_ALL=C
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sed -i 's/$/ universe/' /etc/apt/sources.list
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apt-get update
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apt-get -y install \
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binutils \
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build-essential \
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doxygen \
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doxypy \
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f2c \
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g++ \
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gcc \
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gfortran \
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git \
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graphviz \
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libblas-dev \
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liblapack-dev \
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libopenmpi-dev \
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make \
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openmpi-bin \
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openmpi-common \
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sqlite3 \
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swig \
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wget
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apt-get clean
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
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bash ~/miniconda.sh -b -p /usr/local/miniconda3
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export PATH="/usr/local/miniconda3/bin:$PATH"
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conda create -q --yes -n pmsco python=${PYTHON_VERSION}
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. /usr/local/miniconda3/bin/activate pmsco
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conda install -q --yes -n pmsco \
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pip \
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numpy \
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scipy \
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ipython \
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mpi4py \
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matplotlib \
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nose \
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mock \
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future \
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statsmodels
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conda clean --all -y
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/usr/local/miniconda3/envs/pmsco/bin/pip install periodictable attrdict fasteners
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#%test
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# test the image after build
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%runscript
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# executes command from command line
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source /usr/local/miniconda3/bin/activate pmsco
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exec echo "$@"
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%apprun install
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source /usr/local/miniconda3/bin/activate pmsco
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cd ~
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git clone https://git.psi.ch/pearl/pmsco.git pmsco
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cd pmsco
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git checkout develop
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git checkout -b ${SINGULAR_BRANCH}
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make all
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nosetests
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%apprun python
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source /usr/local/miniconda3/bin/activate pmsco
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exec python "${@}"
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%apprun conda
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source /usr/local/miniconda3/bin/activate pmsco
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exec conda "${@}"
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