Number of GPU threads in V2

Is there a way to increase the number of threads that run on a GPU? V2 seems more inefficient than V1, does not seem to use the GPU to the max (when monitored with nvidia-smi). In V1 I had ab-initio reconstructions finish in 10-20 minutes, now a similar job took 3 hours. Also, ab-initio uses a single GPU, there are no other options.