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Starting with 2016.3 RubyMine uses rsync utility to speed up gem downloading in case remote interpreters are configured for an application.

Rsync is used by default while gem downloading if it is installed on a local machine. To switch it off please uncheck Registry option 'ide.remote.interpreters.use.rsync':

Gem downloading with rsync

No matter you use a prepared Deployment configuration or SSH credentials to set up a remote Ruby interpreter configuration, rsync is being used. When setting up with SSH credentials we recommend to use certificates by choosing 'Key pair (OpenSSH or PuTTy)' in Auth type field. You can also provide a password by choosing 'Password' accordingly. When password is provided, RubyMine emulates Terminal to use it (the command looks like: rsync -zarv user@host:/remote/path /local/path).

RubyMine informs you if rsync is not installed on a local machine:

Installing rsync

Linux

sudo apt-get -y install rsync

OS X

Rsync is installed by default.

Windows 

Windows: can be used on Windows systems but is only available through various ports (such as Cygwin).