Is there any way to get burnup chart build for the whole project (i.e. across all the versions)? I use Jira with GreenHopper plugin 4.3
The key is setting up your versions appropriately.
My setup might work for you (at least as an inspiration)
I have a top level version for the complete project.
Then I have bunch of release version, which are chunks that are intended to get actually released to the customer. Each having the 'complete project' version as parent. You can define that in the planning board view on the version card thingies.
And finally I have a version for each sprint have the appropriate release version as parent.
With this setup I can select versions on every level in the chart view and it works as expected.
Note that if you finish tasks and afterwards change parents of versions the tasks don't get updated accordingly so your diagrams might be confusing.