It is always quite the difficult to provide accurate answers with only a glimpse of the system, but have you actually tried to check the actual throughput ?
As a first solution, I would simply recommend using a dedicated disk (so there are no concurrent read/write actions from other processes), and a fast one at that. This way it would be just some cost of hardware upgrade, and we all know hardware is usually cheaper that software ;) You may even go to a RAID controller for maximizing throughput.
If you are still limited by the disk throughput, there are new technologies out there using the Flash technology: USB keys (though it may not seem very professional) or the "new" Solid State Drives may provide more throughput than a mechanical disk.
Now, if the disks approach are not fast enough or you can't get your hands on good SSDs, you have other solutions, but they involve software changes, and I propose them off the top of my hat.
- A socket approach: the second utility is listening on a port and you send it the data there. On a local machine it's relatively fast, and you parallelize the work too, so even if the size of the data grows, you will still begin treating fairly quickly.
- A memory mapping approach: write to a dedicated area in live memory and have the utility read from that area (Boost.Interprocess may help, there are other solutions).
Note that if the read is sequential, I find it more "natural" to try a 'pipe' approach (ala Unix) so that the two processes execute concurrently. In a traditional pipe, the data may not hit the disk after all.
A shame, isn't it, that in this age of overwhelming processing power, we are still struggling with our disk IO ?