Added some more VM stuff.

tools/Vagrantfile

+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "chef/centos-6.5"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  config.vm.provision "shell",
+      inline: "su -c 'source /vagrant/setup_centos_vm.sh' vagrant"
+  
+end

tools/build_conda_package_vagrant.sh

+export PATH=$HOME/miniconda/bin:$PATH
+export SWIG_LIB=$HOME/miniconda/share/swig/
+export CC="clang++"
+
+git clone -b vagrant https://github.com/kyleabeauchamp/openmm.git
+cd openmm
+conda install --file tools/ci/requirements-conda.txt --yes
+conda build tools/conda-recipe

tools/setup_centos_vm.sh

@@ -6,7 +6,7 @@
 
 
 # Download and enable the EPEL RedHat EL extras repository
-mkdir Software
+mkdir ~/Software
 cd Software
 sudo yum install wget -y
 wget http://mirror.umd.edu/fedora/epel/6/i386/epel-release-6-8.noarch.rpm
@@ -36,33 +36,25 @@ sudo yum install cuda -y
 rm cuda-repo-rhel6-6.0-37.x86_64.rpm
 
 
-# Download AMD APP SDK from here, requires click agreement: http://developer.amd.com/amd-license-agreement-appsdk/
-# Ideally we could cache this on AWS or something...
-mkdir ~/AMD
-cd ~/AMD
-# Copy the tarball to this directory from wherever you got it.
-cp /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz  ./
-tar -zxvf  /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz
-sudo ./Install-AMD-APP.sh
-
+# Install Conda
 cd ~/Software
 wget http://repo.continuum.io/miniconda/Miniconda-3.0.5-Linux-x86_64.sh
 bash Miniconda-3.0.5-Linux-x86_64.sh -b
 
-export PATH=$HOME/miniconda/bin:$PATH
-
+# So there is a bug in some versions of anaconda where the path to swig files is HARDCODED.  Below is workaround.  See https://github.com/ContinuumIO/anaconda-issues/issues/48
+sudo ln -s  ~/miniconda/ /opt/anaconda1anaconda2anaconda3
 
+export PATH=$HOME/miniconda/bin:$PATH
+conda config --add channels http://conda.binstar.org/omnia
+conda install --yes fftw3f jinja2 swig sphinx conda-build cmake
 
-# MANUAL installation below this point###
-# MANUAL installation below this point###
-# MANUAL installation below this point###
 
-conda config --add channels http://conda.binstar.org/omnia
-conda install --yes fftw3f jinja2 swig sphinx conda-build
+# Download AMD APP SDK from here, requires click agreement: http://developer.amd.com/amd-license-agreement-appsdk/
+# Ideally we could cache this on AWS or something...
+mkdir ~/Software/AMD
+cd ~/Software/AMD
+# Copy the tarball to this directory from wherever you got it.
+cp /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz  ./
+tar -zxvf  /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz
+sudo ./Install-AMD-APP.sh
 
-#git clone https://github.com/SimTk/openmm.git
-git clone -b vagrant https://github.com/kyleabeauchamp/openmm.git
-cd openmm
-conda install --file tools/ci/requirements-conda.txt --yes
-export CC="clang++"
-conda build tools/conda-recipe