I have been following the vagrant Getting Started Guide.
I had a problem where vagrant would freeze my entire machine when using vagrant up, so I did what was suggested here (scroll down towards the bottom to a post by Valross.nu).
I have Vagrant 2.0.1 and VirtualBox 5.2.6 installed on Ubuntu 16.04.
When running vagrant init, vagrant up, or pretty much any other command, I get the following errors:
/opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:293:in `read': Input/output error @ rb_sysopen - /home/patrick/.vagrant.d/data/machine-index/index (Errno::EIO) from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:293:in `read' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:293:in `unlocked_reload' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:53:in `block in initialize' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:323:in `block in with_index_lock' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:321:in `open' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:321:in `with_index_lock' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/machine_index.rb:52:in `initialize' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/environment.rb:741:in `new' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/environment.rb:741:in `machine_index' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/environment.rb:215:in `block in action_runner' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/action/runner.rb:33:in `run' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/environment.rb:543:in `hook' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/lib/vagrant/environment.rb:792:in `unload' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/bin/vagrant:141:in `ensure in <main>' from /opt/vagrant/embedded/gems/gems/vagrant-2.0.1/bin/vagrant:141:in `<main>'