Ancients of Days — Paul McAuley

On an artificial world created and seeded with ten thousand bloodlines by the long-vanished Preservers, young Yama's ancestry is unique, for he appears to be the last remaining scion of the Builders, closest of all races to the worshipped architects of Confluence. And on a day near the end of the world, Yama must finally acknowledge the power he neither anticipated nor desires.
In the dust of many crumbling bureaucracies, Yama searches for an identity and a history - awed and fearful of his ever-growing capacity to awaken the terrible machines of destruction that his world's absent gods left slumbering. To the common folk - the unshaped and aboriginal - he is the fulfillment of age-old prophecies. To the functionaries of the Department of Indigenous Affairs, he is a weapon to be molded and used in the bloody civil war raging at the planet's midpoint - a seemingly endless battle that pits those who revere the Preservers' laws against the dangerous Heretics who would obliterate all antiquated values and codes of conduct.
But there are still others who have taken notice of Yama as he pursues the hidden secrets of his past. Intelligent powers older than the Builders - as old, perhaps, as the Preservers themselves - are pursuing Yama in turn. And they will stop at nothing to control his present-and, as a result, the future of everything that lives-in anticipation of the ultimate triumph of the Ancients of Days.