I have studied the FairLink problem in more detail. The problem is the enormous amount of data created for the TPC. For one special event it has: 19281 PrimäriClusters, 42958 Drifted Electrons, 42958 Avalanches, 80300 Signals and 1,674,929 Digis.
All this objects have links to the previous one. I could speed up the linking by a factor of 2 by using std::set instead of std::vector. Nevertheless this one event takes 500 s on my PC. I think that for the TPC one should bypass the linking and only connect the TpcClusters with the MC points and only for dedicated studies one switches on linking.