nishap.pa...@utoronto.ca wrote:
Thanks Justin. But how come it worked for methanol. The system is of the
same size , and all the parameters are same, so I don't understand why
it won't work for ethanol.
I don't know. The DD algorithm is rather complex, and beyond the information in
the manual, I can't really comment. There are additional bonded interactions in
ethanol relative to methanol, which could influence several factors in setting
up the DD algorithm, which you could identify by comparing the DD information
from both the log files.
-Justin
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
nishap.pa...@utoronto.ca wrote:
Hello,
I got this following error when I was trying to run a simulation
of ethanol-water box size 4*4*4 nm (~6530 atoms).
Fatal error:
There is no domain decomposition for 14 nodes that is compatible
with the given box and a minimum cell size of 0.62175 nm
Change the number of nodes or mdrun option -rcon or -dds or your
LINCS settings
Look in the log file for details on the domain decomposition.
I looked into my log file and this is what I got:
Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.234 nm, LJ-14, atoms 1 9
multi-body bonded interactions: 0.234 nm, Angle, atoms 2 5
Minimum cell size due to bonded interactions: 0.257 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans:
0.497 nm
Estimated maximum distance required for P-LINCS: 0.497 nm
This distance will limit the DD cell size, you can override this with
-rcon
Guess for relative PME load: 0.13
Will use 14 particle-particle and 2 PME only nodes
This is a guess, check the performance at the end of the log file
Using 2 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 14 cells with a minimum initial size of
0.622 nm
The maximum allowed number of cells is: X 6 Y 6 Z 6
I am using the same .mdp file that I used for methanol, and it is
working fine, I don't understand why it's giving me problem for
ethanol. I am running my simulation on 2 nodes.
Not according to the log file messages. You're running on 16 nodes,
with 14 for PP and 2 for PME. Your system is of insufficient size to
be divided over this many PP nodes. Check the list archive for tips,
or simply use less nodes for the calculation. There is also
information in the manual about all of the settings that are mentioned
in the log file.
-Justin
Suggestions?
Thanks
-Nisha P
--
========================================
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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========================================
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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