Fabio Affinito wrote:
Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.583 nm, LJ-14, atoms 28051 28056
multi-body bonded interactions: 0.583 nm, Proper Dih., atoms 28051
28056
Minimum cell size due to bonded interactions: 0.642 nm
Maximum distance for 7 constraints, at 120 deg. angles, all-trans:
1.139 nm
Estimated maximum distance required for P-LINCS: 1.139 nm
This distance will limit the DD cell size, you can override this with
-rcon
Guess for relative PME load: 0.43
Will use 2400 particle-particle and 1696 PME only nodes
This is a guess, check the performance at the end of the log file
Using 1696 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2400 cells with a minimum initial size of
1.424 nm
The maximum allowed number of cells is: X 18 Y 18 Z 6
-------------------------------------------------------
Program mdrun_mpi_bg, VERSION 4.5.4
Source code file: domdec.c, line: 6438
Fatal error:
There is no domain decomposition for 2400 nodes that is compatible
with the given box and a minimum cell size of 1.4242 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
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
I imagine that now I have to tune the dds and rcon parameter. Am I right?
I've never touched those parameters and I do not know how they will affect
performance or the stability of your systems. The easier solution is to simply
reduce the number of processors so that the cell sizes increase a bit.
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
--
========================================
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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