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

[Carsten Kutzner]

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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