[gmx-users] REMD slow's down drastically

Christopher Neale chris.neale at alum.utoronto.ca
Mon Feb 24 22:56:29 CET 2014

Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue?

I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run "mpirun -np $N mdrun" where $N is the number of cores

NOTE: The number of threads is not equal to the number of (logical) cores
      and the -pin option is set to auto: will not pin thread to cores.
      This can lead to significant performance degradation.
      Consider using -pin on (and -pinoffset in case you run multiple jobs).

However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting:

"Pinning threads with a logical core stride of 1"

Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though).

Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Singam Karthick <sikart21 at yahoo.in>
Sent: 24 February 2014 02:32
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] REMD slow's down drastically

Dear members,
I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue.

Following is the MDP file

title           = G4Ga3a4a5 production.
;define         = ;-DPOSRES     ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 12500000      ; 2 * 5000000 = 3ns
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 0             ; save coordinates every 0.2 ps
nstvout         = 10000         ; save velocities every 0.2 ps
nstxtcout       = 500           ; save xtc coordinate every 0.2 ps
nstenergy       = 500           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps
; Bond parameters
continuation    = yes           ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = hbonds        ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
morse           = no
; Neighborsearching
ns_type         = grid          ; search neighboring grid cels
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; 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 is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         =  protein SOL Cl       ;two coupling groups - more accurate
tau_t                 = 0.1 0.1  0.1 ; time constant, in ps
ref_t                 = XXXXX  XXXXX  XXXXX    ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in 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

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