Hi Sebastien,
From my experience with similarly sized datasets, something definitely
seems amiss here. relax can at times be very slow, particularly during
grid searches over the ellipsoid diffusion tensor, but I would have
expected the simpler diffusion models to have been through many rounds
within 30 hrs.
To understand what is going on, it would be helpful to know what stage
the various calculations are stuck at (just the last dozen lines written
to each log would be good).
Chris
On Thu, 2006-10-12 at 14:39 -0400, Sebastien Morin wrote:
Hi !
I am trying the script full_analysis.py with my data.
I work with data at three different magnetic fields for 220 residues on
a 271 residue protein.
I successfully ran the script with the local_tm model, and then with all
other diffusion models (sphere, prolate, oblate and ellipsoid) as what
concerns the initial run.
However, the round 1 runs seem to be stuck (or maybe am I too
impatient)... Let me explain with some benchmarks.
Model Round Machine Time
========== ===== =========== =======
local_tm --- Pelican 15h00
-----------------------------------------------
sphere init Pelican 0h10
1 Pelican > 30h00
prolate init Hibou 0h20
1 Hibou > 30h00
oblate init Hibou 0h20
1 Hibou > 30h00
ellipsoid init Pigeon 1h00
1 > 30h00
-----------------------------------------------
final init
Also, I find strange the fact that all sub-directories (m0, m1, m2, m3,
m4, m5, m6, m7, m8, m9 and aic) in those pseudo stuck runs were created
with their bz2 archives more than 24h00 ago...
Moreover, it's been more than 6h00 since nothing hasn't been put in the
log files (which are redirected screen text).
So...
1. Is it normal that these runs take so long to stop ?
2. How can I know that the runs aren't stuck ?
Thank you for your precious help !
Sébastien :)
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Re: full_analysis.py