Satisfying on-demand access to cloud computing infrastructures under quality-of-service constraints while minimising the wastage of resources is an important challenge in data centre resource management. In this paper we tackle this challenge in a semi-online workload management system allocating tasks with uncertain duration to physical servers. Our semi-online framework, based on a bin packing approach, allows us to gather information on incoming tasks during a short time window before deciding on their assignments. Our contributions are as follows: (i) we propose a formal framework capturing the semi-online consolidation problem; (ii) we propose a new dynamic and real-time allocation algorithm based on the incremental merging of bins; and (iii) an adaptation of standard bin packing heuristics with a local search algorithm for the semi-online context considered here. We provide a systematic study of the impact of varying time-period size and varying the degrees of uncertainty on the duration of incoming tasks. The policies are compared in terms of solution quality and solving time on a data-set extracted from a real-world cluster trace. Our results show that, around periods of high demand, our best policy saves up to 40% of the resources compared to the other polices, and is robust to uncertainty in the task durations. Finally, we show that small increases in the allowable time window allows a significant improvement, but that larger time windows do not necessarily improve resource usage for real world data sets.