Merge pull request #52 from fangohr/master

Docker file for fidimag

Author: Weiwei Wang

bin/ubuntu_install_script.sh

@@ -1,5 +1,7 @@
-sudo bash install.sh
 sudo bash install-ubuntu-packages.sh
+bash install-fftw.sh
+bash install-sundials-2.5.sh
 sudo pip install cython --upgrade
+cd ..
 make
 echo "export PYTHONPATH=$(dirname $PWD):$PYTHONPATH" >> /home/$USER/.bashrc

install/docker/Dockerfile

@@ -0,0 +1,61 @@
+FROM ubuntu:14.04
+
+# packages we need to run fidimag
+RUN apt-get -y update
+RUN apt-get -y install python-numpy python-dev python-scipy
+RUN apt-get -y install python-pytest python-pyvtk ipython python-matplotlib mayavi2
+# standard tools for compilation
+RUN apt-get -y install wget make git
+
+# where to install source
+ENV FIDIMAG_HOME /home/fidimag
+
+RUN mkdir -p $FIDIMAG_HOME
+WORKDIR $FIDIMAG_HOME
+RUN git clone https://github.com/computationalmodelling/fidimag.git
+WORKDIR $FIDIMAG_HOME/fidimag/bin
+
+# install third party libraries from source
+RUN bash install-ubuntu-packages.sh
+RUN bash install-fftw.sh
+RUN bash install-sundials-2.5.sh
+
+# for pip
+RUN apt-get -y install python-pip
+# install cython
+RUN pip install cython --upgrade
+WORKDIR $FIDIMAG_HOME/fidimag
+
+# compile fidimag
+RUN make
+env PYTHONPATH=$FIDIMAG_HOME/fidimag
+env LD_LIBRARY_PATH=$FIDIMAG_HOME/fidimag/local/lib
+WORKDIR $FIDIMAG_HOME/fidimag/tests
+
+# check that tests run okay
+RUN py.test -v
+
+
+# install Jupyter, port exposing doesn't work yet
+#RUN pip install jupyter
+
+# expose jupyter port - not working yet
+#EXPOSE 8888 8888
+
+
+# Set up user so that we do not run as root
+RUN useradd -m -s /bin/bash -G sudo fidimag && \
+    echo "fidimag:docker" | chpasswd && \
+    echo "fidimag ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+RUN chown -R fidimag $FIDIMAG_HOME
+
+USER fidimag
+RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
+
+# Print something nice on entry.
+#COPY WELCOME $FIDIMAG_HOME/WELCOME
+
+
+
+WORKDIR $FIDIMAG_HOME
+CMD ["/bin/bash","-i"]

install/docker/Dockerfile.org

@@ -0,0 +1,14 @@
+* How to use
+
+** Linux
+
+$> sudo docker pull fangohr/fidimag
+
+$> docker run -ci fangohr/fidimag ipython
+
+then try 'import fidimag'.
+
+
+
+
+

install/docker/Makefile

@@ -0,0 +1,19 @@
+# to build a new docker image
+build:
+	time docker build -t fangohr/fidimag:latest .
+
+# to run new image
+run:
+	docker run -ti fangohr/fidimag bash
+	# try 'ipython' and then 'import fidimag'
+
+login:
+	docker login
+
+# to push the new docker image to dockerhub (need to login first)
+push:
+	docker push fangohr/fidimag:latest
+
+# to fetch image to local machine
+pull:
+	docker pull fangohr/fidimag:latest

install/docker/Readme.md

@@ -0,0 +1,61 @@
+# Docker
+
+First steps towards running fidimag through Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fangohr/fidimag`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+`docker pull fangohr/fidimag`
+
+3. Start the container using
+
+`docker run -ti fangohr/fidimag`
+
+This command should show a bash prompt inside the docker container:
+
+<pre>
+bin:docker fangohr$ docker run -ti fangohr/fidimag
+fidimag@38fdd2a0feb4:~$
+</pre>
+
+One way to test the installation is to run the unit tests:
+
+<pre>
+fidimag@38fdd2a0feb4:~$ cd fidimag/tests/
+fidimag@38fdd2a0feb4:~/fidimag/tests$ py.test -v 
+========== test session starts =======================
+platform linux2 -- Python 2.7.6 -- pytest-2.5.1 -- /usr/bin/python
+collected 63 items 
+
+field_test.py:7: test_initialise_scalar PASSED
+field_test.py:13: test_initialise_vector PASSED
+test_2dpbc_cube.py:10: test_compute_field PASSED
+test_anis.py:7: test_anis PASSED
+.
+.
+.
+</pre>
+
+## Shortcomings
+
+- need to share directory between host and container (MOUNT or VOLUME)
+
+- make use of jupyter notebook work (as we have seen in FEniCS course): connect port in container to port on host machine (EXPOSE)
+
+
+
+## Creating the docker container
+
+The `Makefile` in this directory shows the relevant targets (build, login, push) to create a new container and push it to the the cloud.
+
+
+
+
+