Question regarding pthread_cond_wait/pthread_cond_signal latencies

[Pedro Gonnet <gonnet@maths.ox.ac.uk>]

Hi guys,

I'm currently working on a shared-memory parallel Molecular Dynamics
simulation library (http://mdcore.sourceforge.net/) geared towards
multi-core systems.

The library uses pthreads (plus some OpenMP for some simple loops) and
uses pthread_cond_wait and pthread_cond_signal to coordinate a group of
worker threads.

I've been profiling the library on different machines and kernels and
have noticed that in many cases there are significant (several ms,
measured with Intel's Vtune-thing) lags between calls to
pthread_cond_signal and the waiting thread actually getting back to
work.

I've tried the Ubuntu -rt and -preempt kernels, and the whole simulation
runs twice as slowly, despite following the advice given here:

        https://rt.wiki.kernel.org/index.php/HOWTO:_Build_an_RT-application

My question is the following: which kernel (or set of configuration
options) will minimize these latencies? And if linux-rt is the answer,
in what ways do I have to be careful when porting the simulation for
this kernel?

Cheers and thanks,
Pedro