[WIP] Updates for OpenMM 7.0

linux/Vagrantfile

@@ -10,7 +10,8 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
   # please see the online documentation at vagrantup.com.
 
   # Every Vagrant virtual environment requires a box to build off of.
-  config.vm.box = "chef/centos-6.6"
+  #config.vm.box = "chef/centos-6.6"
+  config.vm.box = "bento/centos-6.7"
 
   # Disable automatic box update checking. If you disable this, then
   # boxes will only be checked for updates when the user runs
@@ -84,5 +85,5 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
 
   config.vm.provision "shell",
       inline: "su -c 'bash -x /vagrant/setup_centos_vm.sh' vagrant"
-  
+
 end

linux/setup_centos_vm.sh

@@ -9,22 +9,52 @@ wget --quiet http://dl.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch
 sudo rpm -i --quiet epel-release-6-8.noarch.rpm
 
 # Install things needed for virtualbox guest additions.
-echo "********** Removing old kernel package..."
+sudo yum install -y dkms
+#echo "********** Removing old kernel package..."
 #sudo yum remove -y --quiet kernel-2.6.32-431.el6.x86_64
-sudo yum remove -y --quiet kernel
-echo "********** Installing kernel headers and dkms for virtualbox guest additions..."
-sudo yum install -y --quiet kernel-devel dkms
+#sudo yum remove -y --quiet kernel kernel-headers kernel-devel
+#echo "********** Installing kernel headers and dkms for virtualbox guest additions..."
+#sudo yum install -y --quiet kernel-devel dkms
 
 echo "********** Updating yum..."
 sudo yum update -y --quiet
 
+# Install things needed to add virtualbox guest plugins.
+#sudo yum -y --quiet --enablerepo rpmforge install dkms
+#sudo yum -y --quiet groupinstall "Development Tools"
+#sudo yum -y --quiet install kernel-devel
+#sudo yum -y --quiet install kernel-devel-2.6.32-504.el6.x86_64
+#sudo yum -y --quiet install dkms kernel-headers
+#wget http://vault.centos.org/6.6/centosplus/x86_64/Packages/kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm
+#sudo rpm -i --quiet kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm
+#sudo yum -y --quiet --enablerepo centosplus install kernel-devel-2.6.32-504.el6.centos.plus.x86_64.rpm
+
 # Several of these come from the EPEL repo
 echo "********** Installing lots of packages via yum..."
 sudo yum install -y --quiet tar clang cmake graphviz perl flex bison rpm-build texlive texlive-latex ghostscript gcc gcc-c++ git vim emacs swig zip sphinx python-sphinx doxygen screen
 
 # Install GLUT for OpenGL
 sudo yum install -y --quiet freeglut-devel
 
+# Install AMD APP SDK 3.0
+echo "********** Installing AMD APP SDK 3.0..."
+APPSDKFILE="AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2"
+mkdir ~/Software/AMD
+cd ~/Software/AMD
+# Copy the tarball $APPSDKFILE to the directory containing VagrantFile, which will be shared on the guest as /vagrant/
+sudo yum install -y --quiet redhat-lsb
+URL="http://jenkins.choderalab.org/userContent/$APPSDKFILE"
+#echo "Retrieving AMD APP SDK from $URL..."
+#wget --quiet $URL
+cp /vagrant/$APPSDKFILE .
+echo "Unpacking $APPSDKFILE..."
+tar -jxvf  $APPSDKFILE
+echo "Installing $APPSDKFILE..."
+sudo ./AMD-APP-SDK-v3.0.130.135-GA-linux64.sh -- -s -a yes
+export OPENCL_HOME=/opt/AMDAPPSDK-3.0
+export OPENCL_LIBPATH=/opt/AMDAPPSDK-3.0/lib/x86_64
+
+# Doxygen
 echo "********** Compiling recent doxygen..."
 cd ~/Software
 wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.8.src.tar.gz
@@ -93,23 +123,6 @@ export PATH=$HOME/miniconda/bin:$PATH
 conda config --add channels omnia
 conda install --yes --quiet fftw3f jinja2 swig sphinx conda-build cmake anaconda-client pip
 
-# Install AMD APP SDK
-echo "********** Installing AMD APP SDK 3.0..."
-APPSDKFILE="AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2"
-mkdir ~/Software/AMD
-cd ~/Software/AMD
-# Copy the tarball $APPSDKFILE to the directory containing VagrantFile, which will be shared on the guest as /vagrant/
-sudo yum install -y --quiet redhat-lsb
-URL="http://jenkins.choderalab.org/userContent/$APPSDKFILE"
-echo "Retrieving AMD APP SDK from $URL..."
-wget --quiet $URL
-echo "Unpacking $APPSDKFILE..."
-tar -jxvf  $APPSDKFILE
-echo "Installing $APPSDKFILE..."
-sudo ./AMD-APP-SDK-v3.0.130.135-GA-linux64.sh -- -s -a yes
-export OPENCL_HOME=/opt/AMDAPPSDK-3.0 
-export OPENCL_LIBPATH=/opt/AMDAPPSDK-3.0/lib/x86_64
-
 # Add conda to the path.
 echo "********** Adding paths"
 cd ~
@@ -119,3 +132,4 @@ echo "" >> $HOME/.bashrc
 # Install additional packages via pip.
 echo "********** Installing packages via pip..."
 $HOME/miniconda/bin/pip install --quiet sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen
+