[pymvpa] Time for single permutation varies between a few seconds and several minutes

[Jan Derrfuss]

Hi all,

I'm stumped. I'm running a permutation for a searchlight analysis and 
print the time when the individual permutations start. I turns out that 
the onset times are sometimes mere seconds and sometimes several minutes 
apart.

I've played around with setting or not setting nproc, and with varying 
the number of nproc. With more processors, the times decrease, but can 
still amount to minutes. Just as an example, with nproc=20 a permutation 
usually takes about 14 s, but sometimes it might also take 4-6 minutes:
>    Running permutation 0 11:39:27
>    Running permutation 1 11:39:40
>    Running permutation 2 11:40:04
>    Running permutation 3 11:44:30
>    Running permutation 4 11:50:52
>    Running permutation 5 11:51:08
>    Running permutation 6 11:51:21
>    Running permutation 7 11:51:36
>    Running permutation 8 11:51:50
>    Running permutation 9 11:52:08

Interestingly, even when the permutation takes several minutes, top 
shows 20 processors being busy.

Some info about software and hardware:
- Ubuntu 14.04.1 LTS
- Python: 2.7.6
- PyMVPA: 2.3.1
- pprocess: 0.5
- 20 cores with 2 threads per core (40 virtual cores)

Any ideas as to why this might happen would be greatly appreciated!

Jan