You have multiple .root files containing ntuples and wish to merge them in to one. For example, you have 3 files called ntuple.0.root, ntuple.1.root, and ntuple.2.root. The structure of each is identical, for instance:

ntuple.X.root:
  DecayModeOne
    DecayTree
  DecayModeTwo
    DecayTree
  GetIntegratedLuminosity
    LumiTuple

Here, the indentation represents the folder structure, and the deepest elements (DecayTree, LumiTuple) are TTree objects.

To merge these files, use the hadd command (found in $ROOTSYS/bin):

$ hadd ntuple.root ntuple.0.root ntuple.1.root ntuple.2.root

The first argument is the desired output ntuple, the remaing arguments are the files to be merged.

This will produce the following output when using the example structure above:

hadd Target file: ntuple.root
hadd Source file 1: ntuple.0.root
hadd Source file 2: ntuple.1.root
hadd Source file 3: ntuple.2.root
hadd Target path: ntuple.root:/
hadd Target path: ntuple.root:/DecayModeOne
hadd Target path: ntuple.root:/DecayModeTwo
hadd Target path: ntuple.root:/GetIntegratedLuminosity

This can will take some time if you’re merging lots of data (it took me around 40 minutes to merge 120 ntuples with a total size of 20GB).

A Nicer Way

If you’re using a bash-like shell (bash, zsh), then there is an even nicer way of doing things:

$ hadd ntuple.root ntuple.{0..2}.root

The {0..2} part is expanded by the shell to ntuple.0.root ntuple.1.root ntuple.2.root. If you’re not a regular bash/zsh user, you can still take advantage of the feature by executing

$ bash

in your shell and then

$ exit

once you’re done. Note that this new shell may not have $ROOTSYS/bin in its PATH, but can be quickly added.

$ export PATH=/path/to/root/bin:$PATH