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
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