| With computation becoming more and more complex, some rapid growth of the large scale in the fields such as: molecule designing, molecule track energy, chemical process simulation, optimization and environmental science were appeared. For such tremendous calculation tasks, a single computer is not able to complete these computations obviously: one is the limited capability of single processor; the other is those special expensive parallel computers are too expensive and formerly resource have to be abandoned, which is waste. Therefore, it is necessary and realistic meaning for us to develop an effective parallel calculating technology, platform and realizing method for different researchers, at the same time we can use present computer software and hardware resources fully.This paper supported by national natural science fund of China, and we have construct a parallel PC cluster-based system with 2-8 computers; also can extending more computer nodes easily. We use message passing interface (MPI) as a method to program parallel software, then MPICH has been installed and use C langue to call MPI function warehouse. Finally, we have made and realized parallel iterative arithmetic, matrix of two-dimensional and topological arithmetic, three-dimensional topological arithmetic, molecule dynamics simulation and three-dimensional graphics processing parallel programs. On this basis, we have handled .NET Remoting technology to realize distributed computing with different network section in order to interconnect isomerous network and realize large scale environment pollution forecasting model.We carried out a lot of tests, modifications and measurements on parallel PC cluster-based system construct and computational chemistries parallel arithmetic. During concluding and summarizing the research fruits, a lot of usage ideas and methods were finished, in order to different special researcher program application software by modifying, adding and extending modules.
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