[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

[Tsjerk Wassenaar]

Hi Albert,

You are doing neighboursearching every step! So every step all 200
CPUs need to know the how and what of all the other 199. Imagine the
communication overhead. Furthermore, you have 400 atoms per CPU
(neglecting the PME dedication). That will also make communication a
bottle neck. Which, incidentally, will show up when you finish or
terminate the run. According to the md.mdp you posted you're also
using a 1fs time step rather than 2fs.
Try decreasing the number of CPUs, and increasing nst*. Maybe you can
get much better performance if you have an 8- or 12-core around and
use a single machine. Certainly pays off if you need to do replicate
runs anyway.

Cheers,

Tsjerk

On Wed, Mar 28, 2012 at 5:31 PM, Albert <mailmd2011 at gmail.com> wrote:
> Dear:
>
>   I am using gromacs for membrane simulation (under CHARMM36 FF) which
> contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for
> such system with 2 fs time step. And what really astonished is that the
> efficiency for such simulation is only 3ns/day..... I am wondering what
> happen to my system or gromacs? What can I do to fasten the simulation?
>
> here is my md.mdp:
>
> title                    = god!
> cpp                      = /usr/bin/cpp
> include                  =
> define                   =
> integrator               = md
> dt                       = 0.001
> nsteps                   = 100000000
> nstxout                  = 1000000
> nstvout                  = 1000000
> nstlog                   = 1000000
> nstenergy                = 10000
> nstxtcout                = 100000
> xtc_grps                 =
> energygrps         = Protein POPC SOL ION
> nstcalcenergy            = 1
> nstlist                  = 1
> nstcomm                  = 1
> comm_mode                = Linear
> comm-grps                = Protein_POPC    Water_and_ions
> ns_type                  = grid
> rlist                    = 1.2
> rlistlong         = 1.4
> vdwtype             = Switch
> rvdw                     = 1.2
> rvdw_switch         = 0.8
> coulombtype              = pme
> rcoulomb                 = 1.2
> rcoulomb_switch         = 0.0
> fourierspacing         = 0.15
> pme_order         = 4
> DispCorr             = no
> tcoupl                   = nose-hoover
> nhchainlength            = 1
> tc-grps                  = Protein_POPC    Water_and_ions
> tau_t                    = 0.5            0.5
> ref_t                    = 310         310
> Pcoupl                   = parrinello-rahman
> Pcoupltype               = semiisotropic
> tau_p                    = 5.0
> compressibility          = 4.5e-5       4.5e-5
> ref_p                    = 1.0          1.0
> pbc             = xyz
> gen_vel                  = no
> optimize_fft         = no
> constraints              = hbonds
> constraint_algorithm     = Lincs
>
>
>
> Thank you very much
>
> best
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands