[gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

[maria goranovic]

Hi Folks,

My simulation is running too slow. It took 10 wall clock hours (40 cpu
hours) for a short 50 ps simulation of a ~ 23000 atom DPPC bilayer. The
hardware is a 4-cpu core. The installation is gromacs 3.3.1. I have run much
larger systems (~ 160000 atoms) using the same gromacs installation on the
same hardware, and they run much faster than this (200 ps per 40 cpu hours).


Can anybody suggest why this is happening ? Is it because of latency in the
cpu communication? If so, what is the workaround ?

My .mdp script is below.
These are the run commands.

grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o
heat.tpr
mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c heat.gro -e
heat -g heat.log > & heat.out

;###########################################
; heat.mdp
;
title               =  heating
cpp                 =  /usr/bin/cpp
constraints         =  hbonds
constraint_algorithm = lincs
unconstrained_start =  yes
integrator          =  md
nsteps              =  25000
dt                  =  0.002
comm_mode           =  linear
nstxout             =  5000
nstvout             =  5000
nstlog              =  5000
nstenergy           =  5000
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz
; ------------------
coulombtype         = PME
rcoulomb            = 1.0
vdwtype             = cut-off
rlist               = 1.0
rvdw                = 1.0
fourierspacing      = 0.1
pme_order           = 5
ewald_rtol          = 1e-5
; ---------------------------
; Berendsen temperature and preasure coupling
Tcoupl              =  berendsen
tc-grps             =  DPPC  SOL
tau_t               =  0.6      0.6
; i have also tried a tau value of 0.1, but no speed up
ref_t               =  323.0     323.0
Pcoupl              =  berendsen
Pcoupltype          =  semiisotropic
tau_p               =  1.0        1.0
compressibility     =  4.5e-5  4.5e-5
ref_p               =  1.0        1.0
; ---------------------------
gen_vel             =  yes
gen_temp            =  323.0
gen_seed            =  194040
;###########################################

-- 
Maria G.
Technical University of Denmark
Copenhagen
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