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The ATLAS Level-1 Central Trigger (L1CT) system is a central part of ATLAS data-taking and has undergone a major upgrade for Run 2 of the LHC, in order to cope with the expected increase of instantaneous luminosity of a factor of 2 with respect to Run 1. The upgraded hardware offers more flexibility in the trigger decisions due to the double amount of trigger inputs and usable trigger channels. It also provides an interface to the new topological trigger system. Operationally - particularly useful for commissioning, calibration and test runs - it allows concurrent running of up to 3 different subdetector combinations. An overview of the operational software framework of the L1CT system with particular emphasis of the configuration, controls and monitoring aspects is given. The software framework allows a consistent configuration with respect to the ATLAS experiment and the LHC machine, upstream and downstream trigger processors, and the data acquisition. Trigger and dead-time rates are monitored coherently at all stages of processing and are logged by the online computing system for physics analysis, data quality assurance and operational debugging. In addition, the synchronisation of trigger inputs is watched based on bunch-by-bunch trigger information. Several software tools allow to efficiently display the relevant information in the control room in a way useful for shifters and experts. The design of the framework aims at reliability, flexibility, and robustness of the system and takes into account the operational experience gained during Run 1. The Level-1 Central Trigger was successfully operated with high efficiency during the cosmic-ray, beam-splash and first collision data taking with the full ATLAS detector

Operation of the Upgraded ATLAS Level-1 Central Trigger System