hello guys:
thank you very much for kind reply.
I am not sure about the thread version since there is only bigsize
version of it. And the administrator told me that I have to use the
multiples of 32 in the bg_size parameter. The number specified in "-np"
should be 4 times bg_size.
Probably I should compile it by myself. Does anybody have any idea
how to compile gromacs in blue gene?
thank you very much
Albert
On 04/25/2012 12:31 AM, Dr. Vitaly V. Chaban 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?
Albert -
What is the speed using serial gromacs for the same system?
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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