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

[maria goranovic]

Dear All,

My apologies. I had too big a simulation cell, and too few atoms, hence the
problem.

No particular reason to choose order 5. I will try with pme_order 4 and see
if it improves performance anyway.

thanks !

-maria

On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> Am 24.03.2008 um 10:17 schrieb 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 ?
> Is there a special reason for using pme_order=5? I would use the
> default, 4 instead, or at least an even number.
>
> Carsten
>
> > 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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