The ATLAS data acquisition system is based on O(2k) processing nodes, interconnected by a multi-layer Gigabit Ethernet network. About 20k applications provide the needed capabilities in terms of run control, event selection, data flow, local storage and data monitoring. The whole system has been successfully commissioned during the last two years with cosmic ray and calibration data and it turned out to be robust and reliable. Nevertheless, the continuous operation with beams, the concurrent trigger commissioning, and the understanding of detector and physics performance pose new challenges. The flexibility of the data acquisition infrastructure will be probed and exploited, in order to comply with unexperienced working conditions in terms of data flow, monitoring and configuration requirements. The goal is to minimise both downtime and dead-time, allowing for runtime reconfiguration of the data acquisition and sub-detectors systems as well as for automatic error handling and recovery.
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