[gmx-users] gromacs 4.6 mpirun mdrun_mpi poor output performance

[shubhandra tripathi]

Dear gmx users,
I have problem regarding poor output performace from gromacs-4.6 simulation
via mpirun. I have tried various options but unable to boost performace.
Below command with -npme (32,48,64) combinations was also used with no
improvement in performance.

*"mpirun -np 128  /app/gromacs462/bin/mdrun_mpi -deffnm md " *

the main issue is that load imbalance is very high, causing poor output of
200-500ps per day.

Thanking you

Sincerely,


-----md.log ------
https://drive.google.com/open?id=0B9Gtd3wzhkmPSmk2X1QyYmVlV0k


------PBS script-----
#!/bin/bash
#PBS -l walltime=48:00:00
#PBS -N test1
#PBS -q workq
#PBS -l select=8:ncpus=16:mpiprocs=16
# Go to the directory from which you submitted the job

cd $PBS_O_WORKDIR

source /usr/share/Modules/init/sh
export MPI_DEBUG=all
export MPI_IB_RAILS=2
export MPI_DSM_DISTRIBUTE=1
export MPI_VERBOSE=1
export MPI_BUFS_THRESHOLD=1
export MPI_BUFS_PER_PROC=1024

module load gromacs-4.6.2
module load intel-cluster-studio-2013

mpirun -np 128  /app/gromacs462/bin/mdrun_mpi -deffnm md

----md.mdp----

title       = Protein-ligand complex NVT equilibration
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000000    ; 2 * 50000000 = 100000 ps (100 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 25000         ; suppress .trr output
nstvout     = 25000         ; suppress .trr output
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 10000      ; write .xtc trajectory every 2 ps
energygrps  = Protein GTP
; Bond parameters
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 6             ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type     = grid      ; search neighboring grid cells
nstlist     = 10         ; 10 fs
   ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_GTP Water_and_ions    ; two coupling groups - more
accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution

Regards
Shubhandra