Merge branch 'master' of github.com:computationalmodelling/fidimag

.gitignore

@@ -25,17 +25,13 @@ vtks
 
 
 # ignore *.so created by cython
-fidimag/extensions/baryakhtar_clib.so
-fidimag/extensions/clib.so
-fidimag/extensions/cvode.so
-fidimag/extensions/dipolar.so
-fidimag/extensions/micro_clib.so
-fidimag/extensions/neb_clib.so
-
+fidimag/extensions/*.so
 
 # ignore output from coverage
 htmlcov
 
 # ignore junit test output
 test-reports
 
+# ignore notebook checkpoint directory
+.ipynb_checkpoints/

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

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

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

@@ -1,19 +1,16 @@
 # to build a new docker image
 build:
-	time docker build -t fangohr/fidimag:latest .
+	time docker build -t fidimag/minimal-py2:latest .
 
 # to run new image
-run:
-	docker run -ti fangohr/fidimag bash
+run: build
+	docker run -v `pwd`:/io -ti fidimag/minimal-py2
 	# 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
+push: build
+	docker push fidimag/minimal-py2:latest
 
 # to fetch image to local machine
 pull:
-	docker pull fangohr/fidimag:latest
+	docker pull fidimag/minimal-py2:latest

docker/minimal-py2/Readme.md

@@ -0,0 +1,31 @@
+# Docker
+
+Run fidimag with Python 2 under Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fidimag/minimal-py2`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+       docker pull fidimag/minimal-py2
+
+3. Start the container using
+
+       docker run -ti fidimag/minimal-py2
+
+   This command should show a bash prompt inside the docker container:
+
+    <pre>
+    bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py2
+    fidimag@38fdd2a0feb4:/io$
+    </pre>
+
+## 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.

docker/minimal-py3/Dockerfile

@@ -0,0 +1,64 @@
+FROM ubuntu:14.04
+
+# packages we need to run fidimag
+RUN apt-get -y update
+RUN apt-get -y install python3-numpy python3-dev python3-scipy
+RUN apt-get -y install python3-pytest ipython3 python3-matplotlib python3-pip
+# 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-fftw.sh
+RUN bash install-sundials-2.5.sh
+
+# for pip
+RUN python3 -m pip install --user --upgrade setuptools pip
+# install pyvtk
+RUN python3 -m pip install pyvtk
+# install cython
+RUN python3 -m pip install cython --upgrade
+WORKDIR $FIDIMAG_HOME/fidimag
+
+# compile fidimag
+RUN python3 setup.py build_ext --inplace
+env PYTHONPATH=$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-3 -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
+
+# For bind mounts from host
+RUN mkdir /io
+RUN chown -R fidimag /io
+
+USER fidimag
+RUN touch $FIDIMAG_HOME/.sudo_as_admin_successful
+
+# Print something nice on entry.
+#COPY WELCOME $FIDIMAG_HOME/WELCOME
+
+WORKDIR /io
+CMD ["/bin/bash","-i"]

docker/minimal-py3/Makefile

@@ -0,0 +1,16 @@
+# to build a new docker image
+build:
+	time docker build -t fidimag/minimal-py3:latest .
+
+# to run new image
+run: build
+	docker run -v `pwd`:/io -ti fidimag/minimal-py3
+	# try 'ipython3' and then 'import fidimag'
+
+# to push the new docker image to dockerhub (need to login first)
+push: build
+	docker push fidimag/minimal-py3:latest
+
+# to fetch image to local machine
+pull:
+	docker pull fidimag/minimal-py3:latest

docker/minimal-py3/Readme.md

@@ -0,0 +1,31 @@
+# Docker
+
+Run fidimag with Python 3 under Docker.
+
+## Using the docker container
+
+There is a fidimag container available under `fidimag/minimal-py3`.
+
+To use it, you can try this:
+
+1. Install docker
+
+2. Pull the container onto your machine using
+
+       docker pull fidimag/minimal-py3
+
+3. Start the container using
+
+       docker run -ti fidimag/minimal-py3
+
+   This command should show a bash prompt inside the docker container:
+
+    <pre>
+    bin:docker fangohr$ docker run -v `pwd`:/io -ti fidimag/minimal-py3
+    fidimag@38fdd2a0feb4:/io$
+    </pre>
+
+## 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.

docker/notebook/Dockerfile

@@ -0,0 +1,37 @@
+FROM jupyter/scipy-notebook
+
+# where to install source
+ENV FIDIMAG_DIR $HOME/work/fidimag
+
+RUN git clone https://github.com/computationalmodelling/fidimag.git
+WORKDIR $FIDIMAG_DIR
+
+# install third party libraries from source
+RUN bash bin/install-fftw.sh
+RUN bash bin/install-sundials-2.5.sh
+
+# install pyvtk
+RUN pip install pyvtk
+# install cython
+RUN pip install cython --upgrade
+
+# compile fidimag
+RUN python3 setup.py build_ext --inplace
+ENV PYTHONPATH=$FIDIMAG_DIR
+ENV LD_LIBRARY_PATH=$FIDIMAG_DIR/local/lib
+WORKDIR $FIDIMAG_DIR/tests
+
+# https://github.com/conda-forge/matplotlib-feedstock/issues/36
+RUN conda install --quiet --yes icu
+
+# check that tests run okay
+RUN conda install --quiet --yes pytest
+RUN py.test -v
+
+# /io will be mounted from the host system
+USER root
+RUN mkdir /io
+RUN chown -R $NB_USER /io
+USER $NB_USER
+
+WORKDIR /io

docker/notebook/Makefile

@@ -0,0 +1,15 @@
+# to build a new docker image
+build:
+	time docker build -t fidimag/notebook:latest .
+
+# to run new image
+run: build
+	docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
+
+# to push the new docker image to dockerhub (need to login first)
+push: build
+	docker push fidimag/notebook:latest
+
+# to fetch image to local machine
+pull:
+	docker pull fidimag/notebook:latest

docker/notebook/Readme.md

@@ -0,0 +1,42 @@
+# 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 fidimag/notebook
+
+3. Start the container using
+
+       docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
+
+   This will start a notebook server. You can see it in your browser at
+http://localhost:30008/ on Linux, or http://192.168.99.100:30008/ on Mac (you may
+need to change this IP address if your docker VM is at a different address).
+
+To run a shell instead of the notebook server, run:
+
+    docker run -v `pwd`:/io -ti fidimag/notebook bash
+
+## Shortcomings
+
+- need to share directory between host and container (MOUNT or VOLUME)
+
+
+## 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.
+
+
+
+
+

fidimag/atomistic/anisotropy.py

@@ -44,7 +44,7 @@ class Anisotropy(Energy):
 
     """
 
-    def __init__(self, Ku, axis=(1, 0, 0), name='anis'):
+    def __init__(self, Ku, axis=(1, 0, 0), name='Anisotropy'):
         self.Ku = Ku
         self.name = name
         self.axis = axis

fidimag/atomistic/demag.py

@@ -33,7 +33,7 @@ class Demag(object):
 
     """
 
-    def __init__(self, name='demag'):
+    def __init__(self, name='Demag'):
         self.name = name
         self.jac = True
 

fidimag/atomistic/demag_full.py

@@ -14,7 +14,7 @@ class DemagFull(Energy):
     the energy density.
     """
 
-    def __init__(self, name='demag_full'):
+    def __init__(self, name='DemagFull'):
         self.name = name
         self.jac = True
 

fidimag/atomistic/demag_hexagonal.py

@@ -47,7 +47,7 @@ class DemagHexagonal(object):
 
     """
 
-    def __init__(self, name='demag_hex'):
+    def __init__(self, name='DemagHexagonal'):
         self.name = name
         self.jac = True
 

fidimag/atomistic/exchange.py

@@ -41,7 +41,7 @@ class UniformExchange(Energy):
 
     """
 
-    def __init__(self, J=0, name='exch'):
+    def __init__(self, J=0, name='UniformExchange'):
         self.J = J
         self.name = name
 
@@ -142,7 +142,7 @@ def my_exchange(pos):
 
     """
 
-    def __init__(self, J_fun, name='exch'):
+    def __init__(self, J_fun, name='Exchange'):
         self.J_fun = J_fun
         self.name = name
         self.jac = False