On 16/04/2010 12:02 AM, Shuangxing Dai wrote:
Hi, gmx-users:
I am using latest version of gromacs and found it was really slow. I
was wondering anyone got the same experience and can point out where the
problem is.
I was running double precision for MD. But for each dynamics
simulation, it takes 4 days. I should only take two or three hours.
Well, double precisions is slower - possibly very much so. You need
twice the bus and cache bandwidth because you are throwing around twice
the memory. Otherwise, we can't say much because we don't know anything
about your hardware or where you got your benchmark from.
Other comments below. It looks very much like you've gone and made a
bunch of semi-random changes to things. That's not normally a good idea.
Here is the .mdp file:
define =
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and timestep in ps =
tinit = 0
dt = 0.001
nsteps = 200000
; number of steps for center of mass motion removal =
nstcomm = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 0
nstvout = 0
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 100
xtc-precision = 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 50
; ns algorithm (simple or grid) =
ns_type = grid
;OPTIONS FOR PRESSURE COUPLING
Pcoupl = berendsen
tau_p = 1
compressibility = 4.5e-05
ref_p = 0.1
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps = system
tau_t = 0.1
ref_t = 300
; OPTIONS FOR BONDS =
constraints = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start = no
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 12
That's huge, and the use of lincs is somewhat inconsistent with a 1fs
timestep.
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
rlist = 1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Ewald
This could be a correct decision, but it's unlikely.
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-4
Again, could be correct, or could just be killing you.
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
Mark
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