[gmx-users] REMD slow's down drastically

[Mark Abraham]

On Feb 24, 2014 11:01 PM, "Christopher Neale" <chris.neale at alum.utoronto.ca>
wrote:
>
> 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?

Yes, but part of the larger problem of over-loading the physical cores.

> 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).

Hyper-threading is good for applications that are memory- or user-bound (so
enabled by default on consumer machines), so they can take advantage of CPU
instruction-issue opportunities while stalled. GROMACS kernels are already
CPU-bound, so there is little to gain and it generally does not pay for the
overhead. Generally, one should not use HT; turning it off can be emulated
with the right use of -pinoffset and using half the number of threads.

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

Indeed.

Mark

> Chris.
> ________________________________________
> 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
>
>
> regards
> singam
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