Transfering files
The most common way of transferring files between local and remote locations (and the easiest if you're just starting) is the scp command.
For istance, if you want to send a opt.inp file located at ~/geem/projects to a /home/your_user/projects/ folder located in jupiter:
$ scp ~/geem/projects/opt.inp jupiter:/home/your_user/projects/
This comes from:
$ scp -P 2222 ~/geem/projects/opt.inp USERNAME@150.162.31.2:/home/your_user/projects/
Or the other way around, from jupiter to your local folder:
$ scp jupiter:/home/your_user/projects/opt.out ~/geem/projects/
There are other options (for instance, rclone) that can be also be used to sync files between your local machine and jupiter.
If you're using a windows machine, a good graphical interface that allows you to drag and drop files is mobaxterm.
Vinicius also has a script that syncs and submits jobs while in your local machine, any questions talk to him.