[gmx-users] restarting a sorted shuffled trajectory
steletch at jouy.inra.fr
Tue Feb 27 11:01:07 CET 2007
chris.neale at utoronto.ca a écrit :
Thanks a lot for you all, i realise i haven't posted i found the
solution of my problem, as pointed by Yang Ye (thanks). My problem was
that i used the wrong .top and .gro (the sorted and shuffled one) file
with the sorted, shuffled trr. The discrepancy came from the
pre-processed .tpr (since one need to provide the .top and .gro linked
into the processed .tpr tpr).
Problem solved, run done (still need a lot of work, though ;-).
However, you remark (see below) about the diminution of performance
according to the initial sort over time is very interesting and i'll
probably give it a try to improve scaling (on a single machine with 4
processors, the relative performance is reported to be 78%, i would
expect something close to 100%).
> The benefit of sort tends to deteriorate over time so I find it best to
> do cycles of
> about 200ps. This said, shuffling and sorting my runs gives me 100%
> efficiency to 4cpus =
> they run 4x as fast as they do on a single node. I can't come anywhere
> near that with
> plain runs.
Thanks a lot for your time and answers,
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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