Novel paradigm of Sleptsov Net Computing (SNC) mends imperfections of modern HPC architecture with computing memory implementation and provides a vivid graphical language, fine granulation of concurrent processes, and wide application of formal methods for reliable software design. IDE and VM for SNC have been developed and described in early papers. In the present paper, we considerably reduce GPU memory and thread consumption of the previous prototype implementation, introducing a matrix with condensed columns (MCC), and enhance performance, using the first fireable transition choice on the transition sequence reordered according to the lattice of priorities. MCC takes into consideration procedures of Sleptsov net (SN) arcs processing to enhance performance with rather little overhead compared to traditional sparse matrix formats. We represent a matrix of SN arcs by a pair of considerably smaller matrices, having the same number of columns, with the number of rows equal to the maximal number of nonzero elements over the source matrix columns. The first matrix contains the indexes within the source matrix, the second matrix contains the values within the source matrix. To run an SN, we use the corresponding rectangular matrix of GPU threads, with very few indirect memory accesses via MCC. As a result, we increase VM performance in 2–4 times, and reduce by hundred times GPU memory and thread consumption on programs from the SN software collection.