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fangohrfangohr
committedJul 8, 2016
Merge branch 'master' of github.com:computationalmodelling/fidimag
·
v3.03.0a2
2 parents a56166f + 49a4d00 commit 607aad3

24 files changed

+494
-215
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‎.gitignore

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# ignore *.so created by cython
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fidimag/extensions/baryakhtar_clib.so
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fidimag/extensions/clib.so
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fidimag/extensions/cvode.so
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fidimag/extensions/dipolar.so
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fidimag/extensions/micro_clib.so
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fidimag/extensions/neb_clib.so
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fidimag/extensions/*.so
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# ignore output from coverage
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htmlcov
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# ignore junit test output
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test-reports
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# ignore notebook checkpoint directory
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.ipynb_checkpoints/

‎install/docker/Dockerfile ‎docker/minimal-py2/Dockerfile

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@@ -49,13 +49,16 @@ RUN useradd -m -s /bin/bash -G sudo fidimag && \
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echo "fidimag ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
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RUN chown -R fidimag $FIDIMAG_HOME
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# For bind mounts from host
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RUN mkdir /io
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RUN chown -R fidimag /io
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USER fidimag
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RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
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# Print something nice on entry.
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#COPY WELCOME $FIDIMAG_HOME/WELCOME
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WORKDIR $FIDIMAG_HOME
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WORKDIR /io
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CMD ["/bin/bash","-i"]

‎install/docker/Dockerfile.org ‎docker/minimal-py2/Dockerfile.org

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‎install/docker/Makefile ‎docker/minimal-py2/Makefile

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# to build a new docker image
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build:
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time docker build -t fangohr/fidimag:latest .
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time docker build -t fidimag/minimal-py2:latest .
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# to run new image
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run:
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docker run -ti fangohr/fidimag bash
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run: build
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docker run -v `pwd`:/io -ti fidimag/minimal-py2
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# try 'ipython' and then 'import fidimag'
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login:
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docker login
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# to push the new docker image to dockerhub (need to login first)
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push:
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docker push fangohr/fidimag:latest
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push: build
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docker push fidimag/minimal-py2:latest
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# to fetch image to local machine
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pull:
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docker pull fangohr/fidimag:latest
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docker pull fidimag/minimal-py2:latest

‎docker/minimal-py2/Readme.md

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# Docker
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Run fidimag with Python 2 under Docker.
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## Using the docker container
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There is a fidimag container available under `fidimag/minimal-py2`.
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To use it, you can try this:
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1. Install docker
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2. Pull the container onto your machine using
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docker pull fidimag/minimal-py2
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3. Start the container using
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docker run -ti fidimag/minimal-py2
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This command should show a bash prompt inside the docker container:
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<pre>
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bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py2
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fidimag@38fdd2a0feb4:/io$
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</pre>
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## Creating the docker container
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The `Makefile` in this directory shows the relevant targets (build, login, push)
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to create a new container and push it to the the cloud.

‎docker/minimal-py3/Dockerfile

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FROM ubuntu:14.04
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# packages we need to run fidimag
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RUN apt-get -y update
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RUN apt-get -y install python3-numpy python3-dev python3-scipy
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RUN apt-get -y install python3-pytest ipython3 python3-matplotlib python3-pip
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# standard tools for compilation
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RUN apt-get -y install wget make git
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# where to install source
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ENV FIDIMAG_HOME /home/fidimag
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RUN mkdir -p $FIDIMAG_HOME
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WORKDIR $FIDIMAG_HOME
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RUN git clone https://github.com/computationalmodelling/fidimag.git
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WORKDIR $FIDIMAG_HOME/fidimag/bin
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# install third party libraries from source
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RUN bash install-fftw.sh
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RUN bash install-sundials-2.5.sh
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# for pip
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RUN python3 -m pip install --user --upgrade setuptools pip
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# install pyvtk
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RUN python3 -m pip install pyvtk
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# install cython
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RUN python3 -m pip install cython --upgrade
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WORKDIR $FIDIMAG_HOME/fidimag
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# compile fidimag
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RUN python3 setup.py build_ext --inplace
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env PYTHONPATH=$FIDIMAG_HOME/fidimag
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env LD_LIBRARY_PATH=$FIDIMAG_HOME/fidimag/local/lib
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WORKDIR $FIDIMAG_HOME/fidimag/tests
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# check that tests run okay
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RUN py.test-3 -v
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# install Jupyter, port exposing doesn't work yet
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#RUN pip install jupyter
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# expose jupyter port - not working yet
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#EXPOSE 8888 8888
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# Set up user so that we do not run as root
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RUN useradd -m -s /bin/bash -G sudo fidimag && \
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echo "fidimag:docker" | chpasswd && \
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echo "fidimag ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
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RUN chown -R fidimag $FIDIMAG_HOME
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# For bind mounts from host
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RUN mkdir /io
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RUN chown -R fidimag /io
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USER fidimag
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RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
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# Print something nice on entry.
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#COPY WELCOME $FIDIMAG_HOME/WELCOME
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WORKDIR /io
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CMD ["/bin/bash","-i"]

‎docker/minimal-py3/Makefile

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# to build a new docker image
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build:
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time docker build -t fidimag/minimal-py3:latest .
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# to run new image
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run: build
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docker run -v `pwd`:/io -ti fidimag/minimal-py3
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# try 'ipython3' and then 'import fidimag'
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# to push the new docker image to dockerhub (need to login first)
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push: build
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docker push fidimag/minimal-py3:latest
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# to fetch image to local machine
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pull:
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docker pull fidimag/minimal-py3:latest

‎docker/minimal-py3/Readme.md

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# Docker
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Run fidimag with Python 3 under Docker.
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## Using the docker container
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There is a fidimag container available under `fidimag/minimal-py3`.
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To use it, you can try this:
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1. Install docker
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2. Pull the container onto your machine using
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docker pull fidimag/minimal-py3
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3. Start the container using
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docker run -ti fidimag/minimal-py3
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This command should show a bash prompt inside the docker container:
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<pre>
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bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py3
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fidimag@38fdd2a0feb4:/io$
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</pre>
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## Creating the docker container
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The `Makefile` in this directory shows the relevant targets (build, login, push)
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to create a new container and push it to the the cloud.

‎docker/notebook/Dockerfile

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FROM jupyter/scipy-notebook
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# where to install source
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ENV FIDIMAG_DIR $HOME/work/fidimag
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RUN git clone https://github.com/computationalmodelling/fidimag.git
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WORKDIR $FIDIMAG_DIR
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# install third party libraries from source
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RUN bash bin/install-fftw.sh
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RUN bash bin/install-sundials-2.5.sh
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# install pyvtk
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RUN pip install pyvtk
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# install cython
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RUN pip install cython --upgrade
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# compile fidimag
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RUN python3 setup.py build_ext --inplace
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ENV PYTHONPATH=$FIDIMAG_DIR
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ENV LD_LIBRARY_PATH=$FIDIMAG_DIR/local/lib
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WORKDIR $FIDIMAG_DIR/tests
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# https://github.com/conda-forge/matplotlib-feedstock/issues/36
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RUN conda install --quiet --yes icu
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# check that tests run okay
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RUN conda install --quiet --yes pytest
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RUN py.test -v
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# /io will be mounted from the host system
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USER root
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RUN mkdir /io
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RUN chown -R $NB_USER /io
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USER $NB_USER
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WORKDIR /io

‎docker/notebook/Makefile

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# to build a new docker image
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build:
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time docker build -t fidimag/notebook:latest .
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# to run new image
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run: build
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docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
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# to push the new docker image to dockerhub (need to login first)
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push: build
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docker push fidimag/notebook:latest
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# to fetch image to local machine
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pull:
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docker pull fidimag/notebook:latest

‎docker/notebook/Readme.md

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# Docker
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First steps towards running fidimag through Docker.
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## Using the docker container
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There is a fidimag container available under `fangohr/fidimag`.
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To use it, you can try this:
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1. Install docker
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2. Pull the container onto your machine using
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docker pull fidimag/notebook
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3. Start the container using
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docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
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This will start a notebook server. You can see it in your browser at
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http://localhost:30008/ on Linux, or http://192.168.99.100:30008/ on Mac (you may
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need to change this IP address if your docker VM is at a different address).
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To run a shell instead of the notebook server, run:
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docker run -v `pwd`:/io -ti fidimag/notebook bash
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## Shortcomings
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- need to share directory between host and container (MOUNT or VOLUME)
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## Creating the docker container
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The `Makefile` in this directory shows the relevant targets (build, login, push)
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to create a new container and push it to the the cloud.
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‎fidimag/atomistic/anisotropy.py

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"""
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def __init__(self, Ku, axis=(1, 0, 0), name='anis'):
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def __init__(self, Ku, axis=(1, 0, 0), name='Anisotropy'):
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self.Ku = Ku
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self.name = name
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self.axis = axis

‎fidimag/atomistic/demag.py

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"""
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def __init__(self, name='demag'):
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def __init__(self, name='Demag'):
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self.name = name
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self.jac = True
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‎fidimag/atomistic/demag_full.py

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the energy density.
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"""
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def __init__(self, name='demag_full'):
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def __init__(self, name='DemagFull'):
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self.name = name
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self.jac = True
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‎fidimag/atomistic/demag_hexagonal.py

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"""
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def __init__(self, name='demag_hex'):
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def __init__(self, name='DemagHexagonal'):
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self.name = name
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self.jac = True
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‎fidimag/atomistic/exchange.py

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"""
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def __init__(self, J=0, name='exch'):
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def __init__(self, J=0, name='UniformExchange'):
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self.J = J
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self.name = name
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"""
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def __init__(self, J_fun, name='exch'):
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def __init__(self, J_fun, name='Exchange'):
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self.J_fun = J_fun
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self.name = name
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self.jac = False

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