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

[Justin A. Lemkul]

Albert 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?
> 

Use fewer processors.  You cannot necessarily assign a given system to an 
arbitrary number of processors and expect linear performance increase with the 
number of CPUs.  At some point, the communication overhead exceeds any speedup 
that might be obtained from using more CPUs.  For 80k atoms, I would try some 
benchmarks in the 64-96 CPU range to see how your performance is.  My rule of 
thumb is ~1000 atoms per CPU.  There are considerations for PP:PME node ratio 
when using DD, which also depend on the box type (see the Gromacs 4 paper and 
the manual for more details on such details).

-Justin

> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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