Precision measurements and new physics searches require massive computation in high energy physics experiments. Supercomputer remains one of the most powerful computing resources in various areas. Taking the BESIII experiment as an illustration, we deploy the offline software BOSS into the top-tier supercomputer “Tianhe-II” with the help of Singularity. With very limited internet connection bandwidth and without root privilege, we synchronize and maintain the simulation software up to date through CVMFS successfully, and an acceleration rate in a comparison of HPC and HTC is realized for the same large-scale task. We solve two problems of the real-time internet connection and the conflict of loading locker by a deployment of a squid server and using fuse in memory in each computing node. We provide a MPI python interface for high throughput (HT) parallel computation in Tianhe-II. Meanwhile, the program to deal with data output is also specially aligned so that there is no queue issue in the input/output (I/O) task. The acceleration rate in simulation reaches 80%, as we have done the simulation tests up to 15K processes in parallel.