So, this was the solution, sorry to post it so late, just in case it helps
anyone:

/etc/init.d/ntp stop; date; date `date +"%m%d%H%M%C%y.%S"`; date;
/etc/init.d/ntp start

And tomcat magically switched from 100% CPU to 0.5% :)

From:

https://groups.google.com/forum/?fromgroups#!topic/elasticsearch/_I1_OfaL7QY

[from Michael McCandless help on this thread]

On Sun, Jul 1, 2012 at 6:15 PM, Jack Krupansky <j...@basetechnology.com>wrote:

> Interesting:
>
> "
> The sequence of dates of the UTC second markers will be:
>
> 2012 June 30, 23h 59m 59s
> 2012 June 30, 23h 59m 60s
> 2012 July 1, 0h 0m 0s
> "
>
> See:
> http://wwp.greenwichmeantime.**com/info/leap-second.htm<http://wwp.greenwichmeantime.com/info/leap-second.htm>
>
> So, there were two consecutive second " markers" which were literally
> distinct, but numerically identical.
>
> What "design pattern" for timing did Linux violate? In other words, what
> lesson should we be learning to assure that we don't have a similar problem
> at an application level on a future leap second?
>
> -- Jack Krupansky
>
> -----Original Message----- From: Óscar Marín Miró
> Sent: Sunday, July 01, 2012 11:02 AM
> To: solr-user@lucene.apache.org
> Subject: Re: leap second bug
>
>
> Thanks Michael, nice information :)
>
> On Sun, Jul 1, 2012 at 5:29 PM, Michael McCandless <
> luc...@mikemccandless.com> wrote:
>
>  Looks like this is a low-level Linux issue ... see Shay's email to the
>> ElasticSearch list about it:
>>
>>
>> https://groups.google.com/**forum/?fromgroups#!topic/**
>> elasticsearch/_I1_OfaL7QY<https://groups.google.com/forum/?fromgroups#!topic/elasticsearch/_I1_OfaL7QY>
>>
>> Also see the comments here:
>>
>>      
>> http://news.ycombinator.com/**item?id=4182642<http://news.ycombinator.com/item?id=4182642>
>>
>> Mike McCandless
>>
>> http://blog.mikemccandless.com
>>
>> On Sun, Jul 1, 2012 at 8:08 AM, Óscar Marín Miró
>> <oscarmarinm...@gmail.com> wrote:
>> > Hello Michael, thanks for the note :)
>> >
>> > I'm having a similar problem since yesterday, tomcats are wild on CPU
>> [near
>> > 100%]. Did your solr servers did not reply to index/query requests?
>> >
>> > Thanks :)
>> >
>> > On Sun, Jul 1, 2012 at 1:22 PM, Michael Tsadikov <
>> mich...@myheritage.com
>> >wrote:
>> >
>> >> Our solr servers went into GC hell, and became non-responsive on date
>> >> change today.
>> >>
>> >> Restarting tomcats did not help.
>> >>
>> >> Rebooting the machine did.
>> >>
>> >>
>> >>
>> http://www.wired.com/**wiredenterprise/2012/07/leap-**
>> second-bug-wreaks-havoc-with-**java-linux/<http://www.wired.com/wiredenterprise/2012/07/leap-second-bug-wreaks-havoc-with-java-linux/>
>> >>
>> >
>> >
>> >
>> > --
>> > Whether it's science, technology, personal experience, true love,
>> > astrology, or gut feelings, each of us has confidence in something that
>> we
>> > will never fully comprehend.
>> >  --Roy H. William
>>
>>
>
>
> --
> Whether it's science, technology, personal experience, true love,
> astrology, or gut feelings, each of us has confidence in something that we
> will never fully comprehend.
> --Roy H. William
>



-- 
Whether it's science, technology, personal experience, true love,
astrology, or gut feelings, each of us has confidence in something that we
will never fully comprehend.
 --Roy H. William

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