I noticed similar issue with one of our Jenkins servers

OK, I made a little investigation.
It seems that serialization/de-serialisation in https://github.com/jenkinsci/jacoco-plugin/blob/master/src/main/java/hudson/plugins/jacoco/ExecutionFileLoader.java
takes a lot of cpu, also load doesn't not spread evenly on all cores (I used htop).
In our case I'm speaking about ovirt project (~3800 classes).
iftop doesn't shows significant network traffic and iostat also doesn't shows significant load.
So analyse of the same jacoco.exec file on idle jenkins taking 30-50 seconds, but on production jenkins it can take 30-50 minutes.

This discussion might be relevant to the slow serialisation of .exec files: https://groups.google.com/d/topic/jacoco/4f0rf3zqYKY/discussion

We are also seeing issues where the plugin uses too much CPU and virtual memory on our Oracle Linux 6.4 server.

The class mentioned by Ilia Meerovich is using unbuffered I/O, so I've added a BufferedInputStream: https://github.com/jenkinsci/jacoco-plugin/pull/78

I'm having trouble reproducing the original performance problem, so I haven't seen much difference so far. But perhaps it will help with CPU utilisation when Jenkins is under load. Feedback welcome!

Code changed in jenkins
User: Sean Flanigan
Path:
src/main/java/hudson/plugins/jacoco/ExecutionFileLoader.java
http://jenkins-ci.org/commit/jacoco-plugin/ff66560910e884f10927f3b07e61f24f52d5e2cc
Log:
JENKINS-26254 Use BufferedInputStream to read .exec files

Code changed in jenkins
User: Dominik Stadler
Path:
src/main/java/hudson/plugins/jacoco/ExecutionFileLoader.java
http://jenkins-ci.org/commit/jacoco-plugin/a35ce7309e4ca289bb6045000c400d99e36f4ccf
Log:
Merge pull request #78 from seanf/JENKINS-26254-use-buffer

JENKINS-26254 Use BufferedInputStream to read .exec files

Compare: https://github.com/jenkinsci/jacoco-plugin/compare/c6bf58a4b9d8...a35ce7309e4c

I am closing this for the 2.2.0 release, please report new issues if you still have issues when running with that version of the plugin.