[gmx-users] Parallelization of nose-hoover thermostat.
suzen at theochem.tu-muenchen.de
Thu Apr 25 09:59:19 CEST 2002
Erik Lindahl wrote:
> You mean you get different parallellization performance depending on the
> thermostat you use?
> That sounds a little strange; you will get slightly worse performance if
> you use constraints
> together with Parinello-Rahman coupling, since the constraints have to
> be iterated in this case,
> but an NVT ensemble shouldn't slow things down as far as I know... What
> kind of results do you get?
Specifically speaking, I run same configuration in both ensemble (nve
and nvt hoover).
it is strange because in 4 proc runs, nve runs is about 4 times faster
then nvt run.
Most probably I'm missing someting in parameter files or something else
in .top, that may affect performance this much. Or I really spoiled to
code after my addition of pair potential, but
I didn't touch any parallelization related routines. Or there might be a
compilation procedure was not well gone. I'll extent my test tho.
Down Below is the portion of .mdp file
; Neighbor Searching
nstlist=0 ; frequency of constructing list (zero means once to
ns_type=Simple ; construction method
pbc=no ; periodicity in the system
rlist=0 ; cutoff distance in the short-range neighborlist (nm)
; Electrostatics and VdW
; non-pbc with nstlist and rlist zero
;infinite range all particle contributions will be taken in to account
coulombtype=Cut-Off ; direct calculation by some cut-off
rcoulomb=0 ; all interactions
vdwtype=Cut-Off ; vdw cut_off
rvdw=0 ; no pair pot. cut-off (nm)
DispCorr=no ; dispersion correction
; Temperature Coupling
tc_grps=System ; groups to be coupled
tau_t=1.0 ; time-constant for coupling
ref_t=2773 ; reference temperature
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