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

[Alan Dodd]

The end of the log files after the simulation finishes might help you understand if there's anything odd that's taking more computation than normal.
Also, just one extra running process can slow down the entire simulation as all processors will wait for the slowest.  Check if it takes as long if you run it again.


----- Original Message ----
From: Carsten Kutzner <ckutzne at gwdg.de>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, March 24, 2008 1:19:34 PM
Subject: Re: [gmx-users] Gromacs slow for 23000 atom DPPC bilayer on a (1 x 4) node: 50 ps in 10 hours

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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