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.aghaie
Most 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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
