Merge pull request #709 from kyleabeauchamp/removevm

Removed virtual machine.

devtools/build-vm/linux/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-  # `vagrant box outdated`.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

devtools/build-vm/linux/build_conda_package_vagrant.sh

-export PATH=$HOME/miniconda/bin:$PATH
-export SWIG_LIB=$HOME/miniconda/share/swig/
-export CC="clang++"
-
-git clone https://github.com/simtk/openmm.git
-cd openmm
-git checkout tags/6.1  # To checkout specific release for packaging. 
-conda install --file devtools/ci/requirements-conda.txt --yes
-
-# For CI build:
-conda build devtools/conda-recipe
-
-# For release build:
-cd ../
-git clone https://github.com/omnia-md/conda-recipes.git
-conda build conda-recipes/openmm
-
-# To upload the file, do something the following command but with the package version changed:
-
-binstar upload -u omnia /home/vagrant/miniconda/conda-bld/linux-64/openmm-6.1-py27_0.tar.bz2

devtools/build-vm/linux/setup_centos_vm.sh

-# Prepare a vagrant CentOS 6.5 VM for building OpenMM
-# Needs latest version of vagrant to auto-download the chef package
-#vagrant init chef/centos-6.5
-#vagrant up
-#vagrant ssh
-
-
-# Download and enable the EPEL RedHat EL extras repository
-mkdir ~/Software
-cd Software
-sudo yum install wget -y
-wget http://dl.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
-sudo rpm -i epel-release-6-8.noarch.rpm
-
-sudo yum update -y
-
-# Several of these come from the EPEL repo
-sudo yum install clang cmake28 graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim -y
-# Note: changed from clang-3.4 to clang because the package has apparently been renamed.  KAB Oct 2 2014.  
-
-# Probably can't use RHEL6 version of doxygen because it's very old.
-wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.7.src.tar.gz
-rpmbuild -ta doxygen-1.8.7.src.tar.gz
-sudo rpm -i ~/rpmbuild/RPMS/x86_64/doxygen-1.8.7-1.x86_64.rpm
-rm ~/rpmbuild -r
-
-
-sudo yum clean headers
-sudo yum clean packages
-
-# Install CUDA6.5 for RHEL6
-cd ~/Software
-wget http://developer.download.nvidia.com/compute/cuda/repos/rhel6/x86_64/cuda-repo-rhel6-6.5-14.x86_64.rpm
-sudo rpm -i  cuda-repo-rhel6-6.5-14.x86_64.rpm
-sudo yum clean expire-cache
-sudo yum install cuda -y
-# NOTE: NVIDIA may push new MAJOR release versions of CUDA without warning.
-# This is even *before* doing the below update.  Beware.
-
-sudo yum update -y  # Force a second update, in case CUDA has necessary patches.
-
-# Install Conda
-cd ~/Software
-wget http://repo.continuum.io/miniconda/Miniconda-3.7.0-Linux-x86_64.sh
-bash Miniconda-3.7.0-Linux-x86_64.sh -b
-
-# 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 binstar
-
-
-# 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 the directory containing VagrantFile, which will be shared on the guest as /vagrant/
-cp /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz  ./
-tar -zxvf  /vagrant/AMD-APP-SDK-v2.9-lnx64.tgz
-sudo ./Install-AMD-APP.sh
-