Merging commits from master

Author: davidcorteso

.hgignore

@@ -1 +1 @@
-Weiwei Wang, Marc-Antonio Bisotti, David Cortes, Mark Vousden, Beckie Carey, Marijan Beg, Hans Fangohr
+Weiwei Wang, Marc-Antonio Bisotti, David Cortes, Thomas Kluyver, Mark Vousden, Ryan Pepper, Oliver Laslett, Rebecca Carey, and Hans Fangohr

AUTHORS.txt

@@ -1,5 +1,5 @@
 #!/bin/bash
-echo "HELLO"
+
 # This script installs FFTW locally. It may need to environment
 # variables to work, like 'export CC=gcc' in ARCHER.
 
@@ -33,12 +33,10 @@ download_and_install() {
         tar -xzf ${1}.tar.gz
         cd ${1}
         echo "Configuring "${1}"."
-        ./configure --enable-shared --enable-openmp --prefix=${LIBS_DIR}
+        ./configure --enable-shared --enable-openmp --enable-sse2 --enable-avx --prefix=${LIBS_DIR}
         echo "Compiling and installing "${1}"."
-        {
-            make
-            make install
-        } > /dev/null
+        make
+        make install
         echo "Done."
         cd ${LIBS_DIR}
     fi;

bin/install-fftw.sh

@@ -1,14 +1,17 @@
 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
-
+USER root
+RUN mkdir -p /io
+RUN chown $NB_USER /io
+RUN apt update && apt install -y cmake
+USER $NB_USER
+ENV FIDIMAG_DIR /io
+WORKDIR /io
+RUN git clone https://github.com/rpep/fidimag.git
+WORKDIR /io/fidimag
 # install third party libraries from source
 RUN bash bin/install-fftw.sh
-RUN bash bin/install-sundials-2.5.sh
+RUN bash bin/install-sundials.sh
 
 # install pyvtk
 RUN pip install pyvtk
@@ -17,6 +20,7 @@ RUN pip install cython --upgrade
 
 # compile fidimag
 RUN python3 setup.py build_ext --inplace
+RUN pip install psutil
 ENV PYTHONPATH=$FIDIMAG_DIR
 ENV LD_LIBRARY_PATH=$FIDIMAG_DIR/local/lib
 WORKDIR $FIDIMAG_DIR/tests
@@ -26,12 +30,7 @@ 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/Dockerfile

@@ -16,12 +16,13 @@ To use it, you can try this:
 
 3. Start the container using
 
-       docker run -v `pwd`:/io -d -p 30008:8888 fidimag/notebook
+       docker run -v `pwd`:/io -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
+http://localhost:30008/ on Linux and Mac (you may
 need to change this IP address if your docker VM is at a different address).
 
+You will need to 
 To run a shell instead of the notebook server, run:
 
     docker run -v `pwd`:/io -ti fidimag/notebook bash