On 4/24/12 9:42 AM, Albert wrote:
hello:
I am running a 60,000 atom system with 128 core in a blue gene cluster. and it
is only 1ns/day.... here is the script I used for submitting jobs:
# @ job_name = gmx_test
# @ class = kdm-large
# @ error = gmx_test.err
# @ output = gmx_test.out
# @ wall_clock_limit = 00:20:00
# @ job_type = bluegene
# @ bg_size = 32
# @ queue
mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s npt
_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt" -mode VN -np
128
here is my npt.mdp
title = NPT-01
cpp = /usr/bin/cpp
include =
define = -DPOSRES -DPOSRES_POPE_HEAD
integrator = md
dt = 0.001
nsteps = 5000000
nstxout = 100000
nstvout = 100000
nstlog = 100000
nstenergy = 50000
nstxtcout = 50000
xtc_grps =
energygrps = Protein SOL ION
nstcalcenergy = 10
nstlist = 10
nstcomm = 10
comm_mode = Linear
comm-grps = Protein_POPE Water_and_ions
ns_type = grid
rlist = 1.2
rlistlong = 1.4
vdwtype = Switch
rvdw = 1.2
rvdw_switch = 0.8
coulombtype = pme
rcoulomb = 1.2
rcoulomb_switch = 0.0
fourierspacing = 0.15
pme_order = 6
DispCorr = no
tcoupl = V-rescale ;nose-hoover
nhchainlength = 1
tc-grps = Protein_POPE Water_and_ions
tau_t = 0.1 0.1
ref_t = 310 310
Pcoupl = berendsen ;parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
pbc = xyz
refcoord_scaling = com
gen_vel = no
optimize_fft = no
constraints = hbonds
constraint_algorithm = Lincs
Does anybody have any advices?
The end of the log file will print information about where performance may have
been lost. For 60,000 atoms I would think that 128 cores is too many; you're
sacrificing performance to communication overhead. A good ballpark is 1000
atoms/core. A few quick benchmark calculations should give you a better idea on
the setup for optimal performance.
-Justin
--
========================================
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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