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Hi Daniel and Fabrice,
Intuitively and from experience, I feel and think described problem isn't specifically in core Jenkins codebase, but in configurations of
Fabrice, if you're still seeing the problem as described with current Jenkins version on your Linux systems, then I suggest looking outside of the Jenkins codebase. Earlier, you wrote, "(I did actually never see any linux version not having this problem)"
Since this issue was first created in 2011, since then, computing prices and operating system releases have changed. Per Moore's Law of computing hardware, I suggest that you consider faster hardware, a 64-bit operating system (instead of 32-bit). Linux wise: If you're using Debian, 6.0 squeeze has been superseded by 7.0 wheezy. As for Java, consider using Oracle 1.7 JDK -server with HotSpot VM using -XX:+AggressiveOpts because its performance has been tuned more aggressively when compared to Open JDK defaults. Also, consider Java VM garbage collection parameters -XX:+UseConcMarkSweepGC -XX:+UseParNewGC
Generically speaking, a 100% CPU spike for 1 or more CPU seems like Java garbage collection might be happening due to hundreds of thousands of files being opened and processed and using up Java heap memory (-Xmx). Adding to the complexity: If the system environment only has 1 out of 1 total CPUs being used by other threads, then Jenkins application main thread will seem slow. Specifically, here are configurations in Linux and Java to look for and tune the performance on your system(s).
Linux
Java
Debugging and profiling wise, if you see the 100% CPU issue, you could run: