The paper presented the comparative analysis of the authentication Shnorr’s protocol and the authentication protocol based on the task of finding a Hamilton cycle in the graph. It is shown that with the use of CUDA technology the productivity of protocols on graphs is a shighas Shnorr’s protocol productivity. Theim portance of such research is that protocols on graphs (the authentication protocol on the basis of the proof of graph isomorphism, the authentication protocol based on the task of finding a Hamilton cycle in the graph, etc.) have the property of zero-know ledge proof.