On 18/06/2011 10:36 AM, E. Nihal Korkmaz wrote:
Thanks for the reply.
Would that cause any problems in the simulation?
No.
It says force 154.9%, does that mean it is applying the wrong force?
No, it means calculating the forces is taking an amount of time that is
significantly different from a calculation that had ideal load balance.
Is it safe to proceed to simulation like that?
Yes. Whether you care about efficiency vs throughput is your call to make.
Mark
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>
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