Nick wrote:
Hello Justin,
I forgot to say that with 16 nodes I am getting message below. I search
the list and used -pd option but it takes much much loner than one
processor!
Some systems just don't scale particularly well.
-------------------------------------------------------
Program mdrun, VERSION 4.5.3
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 16 nodes that is compatible with
the given box and a minimum cell size of 4.56121 nm
Change the number of nodes or mdrun option -rdd
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
-------------------------------------------------------
Seems like you've got something weird going on. Most normal systems shouldn't
require such a large cell size.
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
The .log file may provide more useful diagnostic information.
-Justin
On 24 February 2011 16:21, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Nick wrote:
Hello all,
When I issue mdrun program for EM altough this is not a
parallel simulation, 6 nodes are getting involved.
I am using 4.5.3 and get the error:
Reading file em-l0.5.tpr, VERSION 4.5.3 (single precision)
Starting 16 threads
Does anyone have idea why is this happening?
mdrun now uses thread-based parallelization by default, using all
available nodes. To suppress this effect, use mdrun -nt 1.
Otherwise, yes, it is a parallel calculation :)
-Justin
Thanks
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
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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