When I use YJP to do cpu-tracing profile on our own product, it is really slow.
The product runs in a 16 core machine with 8GB heap, and I use grinder to run a small load test (e.g. 10 grinder threads) which have about 7~10 steps during the profiling. I have a script to start the product with profiler, start profiling (using controller api) and then start grinder to emulate user operations. When all the operations finish, the script tells the profiler to stop profiling and save snapshot.
During the profiling, for each step in the grinder test, it takes more than 1 million ms to finish. The whole profiling often takes more than 10 hours with just 10 grinder threads, and each runs the test 10 times. Without profiler, it finishes within 500 ms.
So... besides the problems with the product to be profiled, is there anything else that affects the performance of the cpu tracing process itself?
Last I used YourKit (v7.5.11, which is pretty old, current version is 12) it had two CPU profiling settings: sampling and tracing, the latter being much faster and less accurate. Since tracing is supposed to be more accurate I used it myself and also observed huge slowdown, in spite of the statement that the slowdown were "average". Yet it was far less than your results: from 2 seconds to 10 minutes. My code is a fragment of a calculation engine, virtually no IO, no waits on whatever, just reading a input, calculating and output the result into the console - so the whole slowdown comes from the profiler, no external influences.
Back to your question: the option mentioned - samping vs tracing, will affect the performance, so you may try sampling.
Now that I think of it: YourKit can be setup such that it does things automatically, like making snapshots periodically or on low memory, profiling memory usage, object allocations, each of this measures will make profiling slowlier. Perhaps you should make an online session instead of script controlled, to see what it really does.