On 6/05/2012 7:10 AM, 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?
Those fragments are indicative of -pd.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
