Smart computing aims to improve the quality of life by utilizing Internet-of-Things devices and cloud computing. Typically, this computing handles private and/or personal information so concealing such sensitive information is a challenge. Adopting fully homomorphic encryption (FHE) is one approach for handling such sensitive information safely; that is, we can calculate the encrypted data without decryption. However, the time and space complexity of the FHE operation is high. Thus, its computation takes a long time. In this study, we aim to shorten FHE execution time by adopting our new scheduling algorithm, which divides a task into several macro-tasks and then assigns a set of threads. We assume a cloud computing system that is equipped with a many-core CPU. Thus, we propose the dynamic allocation method of computation resource to macro-tasks (DAMCREM), which dynamically allocates a certain number of threads (selected from pre-defined candidates) to each macro-task of every given job. In the evaluation, we compared DAMCREM to naive methods that allocate a pre-defined number of threads to each macro-task. The result shows that the average latency and maximum latency of job execution is less than those of naive methods, even when the average interval of job arrival is short.