[gmx-users] why it is so slow in Blue gene?

[Albert]

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?

thank you very much