"Program is taking weeks, albeit on a low end server. We used Devel::NYTProf - the biggest chunk of time is writing the output record."

"Any way to reduce this time?"

Without seeing code the only thing I'd add (or rather second) would be, since you care about how fast this happens, don't run it on a "low end" server. Shared servers (VPS etc) often don't give you the performance advertised. PCIe 4 SSDs are just around the corner (a couple of weeks IIRC), up to 5GB/s.