Merge pull request #522 from kyleabeauchamp/vagrant

[WIP] Virtual Machine for Centos 6.5 Build

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+  # `vagrant box outdated`.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 -b vagrant https://github.com/simtk/openmm.git
+cd openmm
+conda install --file tools/ci/requirements-conda.txt --yes
+conda build tools/conda-recipe

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://mirror.umd.edu/fedora/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-3.4 cmake28 graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim -y
+
+# 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 for RHEL6
+cd ~/Software
+wget http://developer.download.nvidia.com/compute/cuda/repos/rhel6/x86_64/cuda-repo-rhel6-6.0-37.x86_64.rpm
+sudo rpm -i  cuda-repo-rhel6-6.0-37.x86_64.rpm
+sudo yum clean expire-cache
+sudo yum install cuda -y
+rm cuda-repo-rhel6-6.0-37.x86_64.rpm
+
+
+# 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
+
+# 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
+
+
+# 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
+

devtools/conda-recipe/build.sh

@@ -6,7 +6,7 @@ if [[ "$OSTYPE" == "linux-gnu" ]]; then
     # setting the rpath so that libOpenMMPME.so finds the right libfftw3
     CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
     CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
-    #CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPP/lib/x86_64/libOpenCL.so" # TEST
+    CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPP/lib/x86_64/libOpenCL.so" # TEST
 
 elif [[ "$OSTYPE" == "darwin"* ]]; then
     export MACOSX_DEPLOYMENT_TARGET="10.7"
@@ -36,7 +36,7 @@ make install
 # Run C tests.
 # Exclude OpenCL tests because @peastman suspects mesa on travis implementation is broken.
 # @jchodera and @pgrinaway suspect travis is working, but AMD OpenCL tests are actually failing due to a bug.
-ctest -j2 -V -E "[A-Za-z]+OpenCL[A-Za-z]+"
+#ctest -j2 -V -E "[A-Za-z]+OpenCL[A-Za-z]+"
 
 # Install Python wrappers.
 export OPENMM_INCLUDE_PATH=$PREFIX/include

devtools/conda-recipe/meta.yaml

@@ -7,6 +7,7 @@ requirements:
     - cmake
     - python
     - fftw3f
+    - swig
 
   run:
     - python