[gmx-users] Determining which parallelization algorithm I used

[Justin A. Lemkul]

On 5/5/12 5:10 PM, Andrew DeYoung wrote:
> Hi,
>
> I think that Gromacs has two parallelization algorithms as of version 4.5:
> domain decomposition (the default) and particle decomposition.
>
> For my research, I am using the particle decomposition algorithm.  Thus, I
> include the -pd switch when calling mdrun.  However, I am worried that in
> one of my runs I forgot to include the -pd switch.  Is there any way to tell
> from the .log file (or anywhere else in the output) which parallelization
> algorithm was used.  When I search for "pd" in the .log file, I see several
> occurrences:
>
> ---
> Division over nodes in atoms:
>      1173    1173    1174    1173    1172    1175
> CPU=  0, lastcg= 1085, targetcg= 3325, myshift=    3
> CPU=  1, lastcg= 1888, targetcg= 4129, myshift=    3
> CPU=  2, lastcg= 2690, targetcg=  450, myshift=    4
> CPU=  3, lastcg= 3494, targetcg= 1254, myshift=    4
> CPU=  4, lastcg= 4244, targetcg= 2004, myshift=    4
> CPU=  5, lastcg= 4479, targetcg= 2240, myshift=    3
> pd->shift =   4, pd->bshift=  0
>
> ...
>
> Workload division
> nnodes:           6
> pd->shift:        4
> pd->bshift:       0
> Nodeid   atom0   #atom     cg0       #cg
>       0       0    1173       0      1086
>       1    1173    1173    1086       803
>       2    2346    1174    1889       802
>       3    3520    1173    2691       804
>       4    4693    1172    3495       750
>       5    5865    1175    4245       235
> ---
>
> Do the mentions of "pd" in the above .log file snippets assure me that I
> indeed used the -pd switch when calling mdrun?
>

Another way to check would be the absence of DD-related information printed to 
the log.  For instance, if you don't see "Initializing domain decomposition on X 
nodes" then it would be apparent that DD wasn't used.

-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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