Merge branch 'master' into ENH-017-skyrmion-number

Author: mvousden

.travis.yml

@@ -22,7 +22,8 @@ install:
   - source activate fidimag-test
   - pip install pyvtk six nbval
   # Download and compile FFTW & Sundials locally
-  - bash bin/install.sh
+  - bash bin/install-sundials-2.5.sh
+  - bash bin/install-fftw.sh
 
 before_script:
         - make build

bin/install-fftw.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+# This script installs FFTW locally. It may need to environment
+# variables to work, like 'export CC=gcc' in ARCHER.
+
+FFTW=fftw-3.3.4
+
+set -e
+
+# Create target directory if needed.
+
+HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+FIDIMAG_DIR="$(dirname "$HERE_DIR")"
+LIBS_DIR=${FIDIMAG_DIR}/local
+mkdir -p $LIBS_DIR
+cd ${LIBS_DIR}
+echo "Installing FFTW to "$LIBS_DIR"."
+echo "Using CC="$CC" "
+
+download_and_install() {
+    # $1 name of the package
+    # $2 URL where ${1}.tar.gz can be obtained
+    # $3 configure options
+    if [ ! -e ${1}.tar.gz ]; then
+        echo "Downloading "${1}"."
+        wget -q ${2}/${1}.tar.gz
+    fi;
+
+    if [ ! -e ${1} ]; then
+        tar -xzf ${1}.tar.gz
+        cd ${1}
+        echo "Configuring "${1}"."
+        ./configure --quiet --enable-shared --enable-openmp --prefix=${LIBS_DIR}
+        echo "Compiling and installing "${1}"."
+        {
+            make
+            make install
+        } > /dev/null
+        echo "Done."
+        cd ${LIBS_DIR}
+    fi;
+}
+
+download_and_install ${FFTW} http://www.fftw.org
+
+echo "Installation succesful."

bin/install.sh bin/install-sundials-2.5.shbin/install.sh renamed to bin/install-sundials-2.5.sh

@@ -1,10 +1,9 @@
 #!/bin/bash
 
-# This script installs SUNDIALS and FFTW locally. It may need to environment
+# This script installs SUNDIALS locally. It may need to environment
 # variables to work, like 'export CC=gcc' in ARCHER.
 
 SUNDIALS=sundials-2.5.0
-FFTW=fftw-3.3.4
 
 set -e
 
@@ -43,6 +42,5 @@ download_and_install() {
 }
 
 download_and_install ${SUNDIALS} http://ftp.mcs.anl.gov/pub/petsc/externalpackages --disable-lapack
-download_and_install ${FFTW} http://www.fftw.org --enable-openmp
 
 echo "Installation succesful."

bin/install-sundials.sh

@@ -61,4 +61,4 @@ download_and_cmake_install() {
 download_and_cmake_install \
     ${SUNDIALS} \
     http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/download \
-    "-DBUILD_STATIC_LIBS=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX="${LIBS_DIR}" -DEXAMPLES_ENABLE=OFF -DLAPACK_ENABLE=ON -DOPENMP_ENABLE=ON"
+    "-DBUILD_STATIC_LIBS=OFF -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX="${LIBS_DIR}" -DEXAMPLES_ENABLE=OFF -DLAPACK_ENABLE=ON -DOPENMP_ENABLE=ON --enable-sse2"

bin/install-ubuntu-packages.sh

@@ -1,4 +1,4 @@
 # required to compile fidimag
-apt-get install python-numpy python-dev python-scipy
+apt-get install python-pip python-numpy python-dev python-scipy
 # required for tests and running it
 apt-get install python-pytest python-pyvtk ipython python-matplotlib

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

doc/index.rst

@@ -19,5 +19,6 @@ Contents:
    install
    core_eqs
    extended_eqs
+   monte_carlo
    develop
    ipynb/tutorial-basics

doc/install.rst

@@ -217,16 +217,18 @@ Notes:
   failed without a working X server).
 
 Install on OS X
-===============
+=================
 
 The inbuilt OS X gcc compiler (actually clang) doesn't have OpenMP support. A workaround is to
 
 - install gcc5 (via homebrew, for example: ``brew install gcc --without-multilib``)
 - set CC environment variable to point to that compiler: ``export CC=gcc-5``
 
+Alternatively, gcc can be installed through ``sudo port install gcc5`` and CC environment 
+variable can be set via ``export CC=gcc-mp-5``
 
-Once this is done, run ``bin/install.sh`` which will compile fftw3 and
-sundials (in a local subdirectory) using this compiler.
+Once this is done, run ``bin/install-fftw.sh`` and ``bin/install-sundials.sh`` which will 
+compile fftw3 and sundials (in a local subdirectory) using this compiler.
 
 Also install pytest (``conda install pytest`` if using conda) and
 ``pyvtk`` via pip (``pip install pyvtk``).