Joe Joe wrote:
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Joe Joe wrote:
How do I determine what those values should be? How does it
affect the simulation?
The header of your log file should have printed what the initial
guesses were. The -dd option sets how many PP nodes there are in the
domain decomposition; using 4 cores, there are probably 3 PP: 1 PME,
so you probably can't tweak this option, really.
I do not get it. the input to -dd is a vector. What to the elements of
the vector represent?
The number of DD grid cells per axis. For example, 3 1 1 means 2 divisions
along the x axis to give 3 DD cells, 1 cell in each the y- and z-axis for a
total of 3 cells. -dd 3 2 1 gives 3 x-cells, 2 y-cells, and 1 z-cell for a
total of 6 DD cells.
The -rcon option is explained in mdrun -h or the manual. See what
mdrun guessed, then increase this value.
I tried -rcon 3.0 and got the same error. The error only occurs when I
do the exchange. If I increase the replex from 500 to 1000 then I do not
see the error for 1000 steps. How is the replex associated with the
domain decomposition?
I don't know the specifics here. There may be some incompatibility between DD
and virtual sites; I know there were some bugs in previous versions. What kind
of virtual sites are you using? Does the run work successfully with -dd turned
off (i.e., mdrun -pd)?
-Justin
-Justin
thanks,
Ilya
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Joe Joe wrote:
Hi All,
I get the following error when running replica exchange.
I have
32 replica's with each replica running on 4 processors (128
total). How do I decrease the domain decomposition cell size,
-dss? What should I set it to?
<snip>
You're getting some hints from mdrun, I'd start there:
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.4
Source code file: domdec_con.c, line: 679
Fatal error:
DD cell 5 0 0 could only obtain 96 of the 108 atoms that are
connected via vsites from the neighboring cells. This
probably
means your vsite lengths are too long compared to the domain
decomposition cell size. Decrease the number of domain
decomposition grid cells or use the -rcon option of mdrun.
-------------------------------------------------------
...So manually set -dd and/or -rcon.
-Justin
-- ========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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