The most reliable way of running benchmarks is to do it in an otherwise idle
system. On a busy system, the results will vary according to the other tasks
demanding attention in the system.

We have managed to obtain quite reliable results by doing the following on 
Linux (and you need root):

 - switching the scheduler to a Real-Time mode
 - setting the processor affinity to one single processor
 - disabling the other thread of the same core

This should work rather well for CPU-intensive tasks. A task that is in Real-
Time mode will simply not be preempted by the OS. But if you make OS syscalls, 
especially I/O ones, your task will be de-scheduled. Note that this includes 
page faults, so if you can, make sure your benchmark's warmup code paths touch 
most of the data.

To do this you need a tool called schedtool (package schedtool), from 
http://freequaos.host.sk/schedtool/

From this point on, we are using CPU0 for all tasks:

If you have a Hyperthreaded multi-core processor (Core-i5 and Core-i7), you 
have to disable the other thread of the same core as CPU0. To discover which 
one it is:

$ cat /sys/devices/system/cpu/cpu0/topology/thread_siblings_list

This will print something like 0,4, meaning that CPUs 0 and 4 are sibling 
threads on the same core. So we'll turn CPU 4 off:

(as root)
# echo 0 > /sys/devices/system/cpu/cpu4/online

To turn it back on, echo 1 into the same file.

To run a task on CPU 0 exclusively, using FIFO RT priority 10, you run the 
following:

(as root)
# schedtool -F -p 10 -a 1 -e ./taskname

For example:
# schedtool -F -p 10 -a 1 -e ./tst_bench_qstring -tickcounter

Warning: if your task livelocks or takes far too long to complete, your system 
may be unusable for a long time, especially if you don't have other cores to 
run stuff on. To prevent that, run it before schedtool and time it.

You can also limit the CPU time that the task is allowed to take. Run in the 
same shell as you'll run schedtool:

$ ulimit -s 300
To limit to 300 seconds (5 minutes)

If your task runs away, it will get a SIGXCPU after consuming 5 minutes of CPU 
time (5 minutes running at 100%).

If your app is multithreaded, you may want to give it more CPUs, like CPU0 and 
CPU1 with -a 3  (it's a bitmask).

For best results, you should disable ALL other cores and threads of the same 
processor. The new Core-i7 have one processor with 4 cores, 
each core can run 2 threads; the older Mac Pros have two processors with 4 
cores each. So on those Mac Pros, you'd disable cores 1, 2 and 3, while on the 
Core-i7, you'll need to disable all other CPUs.

However, disabling just the sibling thread seems to produce very reliable 
results for me already, with variance often below 0.5% (even though there are 
some measurable spikes).

Other things to try:

Running the benchmark with highest priority, i.e. "sudo nice -19" 
usually produces stable results on some machines. If the benchmark also 
involves displaying something on the screen (on X11), running it with 
"-sync" is a must. Though, in that case the "real" cost is not correct, 
but it is useful to discover regressions.

Also; not many people know about ionice (1)
      ionice - get/set program io scheduling class and priority