I have a larger C++ program which starts out by reading thousands of small text files into memory and storing data in stl containers. This takes about a minute. Periodically, a compilation will exhibit behavior where that initial part of the program will run at about 22-23% CPU load. Once that step is over, it goes back to ~100% CPU. It is more likely to happen with O2 flag turned on but not consistently. It happens even less often with the -p flag which makes it almost impossible to profile. I did capture it once but the gprof output wasn't helpful - everything runs with the same relative speed just at low cpu usage.

I am quite certain that this has nothing to do with multiple cores. I do have a quad-core cpu, and most of the code is multi-threaded, but I tested this issue running a single thread. Also, when I run the problematic step in multiple threads, each thread only runs at ~20% CPU.

I apologize ahead of time for the vagueness of the question but I have run out of ideas as to how to troubleshoot it further, so any hints might be helpful.

UPDATE: Just to make sure it's clear, the problematic part of the code does sometimes (~30-40% of the compilations) run at 100% CPU, so it's hard to buy the (otherwise reasonable) argument that I/O is the bottleneck