A scratch folder usually refers to a folder that is fast for reading and writing. If you use a supercomputer, like those in XSEDE or NERSC, you will find out that the SCRATCH folder are the best place to run your simulation (though it is not suggested to store the data there). There may be multiple reseaons that the scratch folder is faster than normal disk. In our own in-house cluster, Fractal, the scratch folder is fast, simply because it is local and large.
Fractal has one main node and multiple compute nodes, where most of the data are stored at four hard disks at the main node...
Read more about Enabling the /scratch folder in a rock system