[gmx-users] Determining which parallelization algorithm I used

[Andrew DeYoung]

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?

Thanks so much for your time!

Andrew DeYoung
Carnegie Mellon University