yywang wrote:
At 2011-12-31 04:42:12,"Justin A. Lemkul" <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
yywang wrote:
Dear Justin Lemkul,
I find a tutorial about the free energy calculation by g_bar in
Gromacs. (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html)
I have a question when I use this tutorail. That is I cannot
use muti-cores in cluster. When I try to use mpirun -np 2 or more, an
error occured (There is no domain decomposition for 2 nodes that is
compatible with the given box and a minimum cell size of 6.46036 nm 228
Change the number of nodes or mdrun option -rdd)
But when i turn the mpirun off ,eg mpirun -np 1 mdrun -nt 2 ,
everything is OK.
I do not know the basis for why MPI vs. threading would lead to different
behavior. I use threading by default on a dual-core machine since the tutorial
system is small.
Since my model is a little big, the speed of use 1 core and 2
threads is too slow, is there any method to change this situation, or do
you know any paramater that control this?
Are we still talking about the tutorial system? It is quite small. The DD cell
size you've posted above seems to be from a different system. I cannot offer
personalized advice for individual systems that I've not worked with. The best
information is online:
>http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
-Justin
Sorry I haven`t express my idea well. I use your tutorial to calculation the
free energy of a big system of my own,which is a big system of 24,0000 atoms,
so this speed is too slow for me and I am trying to run it on big clusters.
Thanks any way.
The simple decoupling procedure in the tutorial is likely not suitable for very
large systems; by changing many degrees of freedom simultaneously in this way,
convergence is exceptionally hard to achieve. I suspect the very large size of
the DD cells is related to the couple-intramol parameter, which for large
systems results in explicit pair interactions, which occur within the same DD
cell. Refer to the manual for a more suitable setting and the reasons why you
might want to adjust certain parameters. Good luck.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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