Introduction: The amount of digital data is constantly growing as well as the need for its storage and processing for various purposes. To conduct data analysis, high-performance computing environments associated with parallelization methods, and, accordingly, dataintensive applications are used. The lack of quality tools for evaluating the effectiveness of the process of parallel data processing or tasks leads to excessive allocation of resources. Purpose: To develop mathematical models of data-intensive computing environments and methods for their performance analysis, i.e., for estimating the average system response time based on the data on system performance at the level of subtask solving. Results: We present a mathematical model of a parallel computing system in the form of a queueing system with parallel query processing on various architectures, including non-Poisson input flow and non-exponential service times. As a method for analyzing the average response time, we use a combination of simulation modeling with one of the machine learning methods (artificial neural networks). The effectiveness of the method is confirmed by numerical experiments and depends neither on the type of input flow, nor on the type of distribution of query service times, nor on the number of servers in the nodes of the system. The approximation error of the average response time does not exceed 10%, which makes it possible to optimize the generally accepted resource allocation, significantly reducing the amount of the resources. Practical relevance: The presented models and the method of their analysis can be used for efficient planning and allocation of resources for data-intensive systems.