E. Nihal Korkmaz wrote:
Thanks for the reply.
Would that cause any problems in the simulation? It says force 154.9%,
does that mean it is applying the wrong force? Is it safe to proceed to
simulation like that?
It just means that one (or maybe more) processors are doing a whole lot more
work than others. There's nothing wrong with the force calculation itself.
For small proteins in an implicit solvent, DD parallelization doesn't offer much
benefit. There are optimized settings for non-periodic systems that may even
result in better performance when there are serious balance issues, in which
case your performance likely isn't very good since the DLB algorithm is clearly
struggling.
-Justin
Thanks,
Nihal
On Thu, Jun 16, 2011 at 9:54 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
__
On 17/06/2011 12:44 PM, E. Nihal Korkmaz wrote:
Hi all,
I am trying to run GB model simulation of a small protein. I keep
getting these errors for every step printed to the log file.
DD load balancing is limited by minimum cell size in dimension X
DD step 35999 vol min/aver 0.799! load imb.: force 154.9%
Not all systems can efficiently parallelize on arbitrary numbers of
processors for a given implementation. There's an analysis at the
top of the .log file that describes the issues leading to the
minimum cell size. Possibly there's an issue there, but more likely
you've got not enough work for your processors.
Mark
Below i copied my mdp parameters. I'd appreciate any suggestion to
help me fix this.
Thanks,
Nihal
integrator = sd
tinit = 0
dt = 0.002
nsteps = 5000000
simulation_part = 1
init_step = 1 %start from 5ns
nstxout = 5000
nstvout = 5000
nstenergy = 500
nstxtcout = 500
nstlog = 500
xtc_grps = System
energygrps = System
comm_mode = Linear
; neighbor searching and vdw/pme setting up
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 2.0
coulombtype = pme
fourierspacing = 0.1
pme_order = 6
rcoulomb = 2.0
vdwtype = Cut-off
rvdw_switch = 1.0
rvdw = 2.0
; cpt control
tcoupl = Berendsen
tc-grps = System
tau_t = 0.1
ref_t = 300.0
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; velocity & temperature control
gen_vel = yes
gen_temp = 300.0
annealing = no
constraints = hbonds
constraint_algorithm = lincs
morse = no
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644 <tel:608-265-3644>
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
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--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
--
========================================
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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