Dear Erik
Thanks for your explanation :)
regards
Delara
--- On Wed, 4/13/11, Erik Marklund <[email protected]> wrote:
From: Erik Marklund <[email protected]>
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: "Discussion list for GROMACS users" <[email protected]>
Date: Wednesday, April 13, 2011, 2:02 PM
delara aghaie skrev 2011-04-13 11.26:
Hello
Previously I used gromacs/3.3 for my simulations of DPPc monolayer+Tip4P2005. I
saw that it uses particle decomposition
Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
This version does the domain decomposition which causes load imbalance.
with this version because of load imbalance and loss of performance the
simulation needs longer time to run.
so the question:
what is the benefit of this domain decomposition. I think it causes the runs to
be done slower !!!.
thanks
D.aghaieMost of the time it reduces communication of coordinates, which in turn
can is one of the big bottlenecks in parallel MD. Domain decomposition makes
sure that atoms which are close to eachother, and hence are likely to interact,
are passed to the same core. With particle decomposition the atoms are
statically asigned to the different cores, and the decomposition may not
reflect how the aroms interact.
Why go for 4.0.7, why not 4.5.4?
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[email protected] http://folding.bmc.uu.se/
-----Inline Attachment Follows-----
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
