[gmx-users] Re: why it is so slow in Blue gene

[Dr. Vitaly V. Chaban]

> hello:
>
>   I am running a 60,000 atom system with 128 core in a blue gene
> cluster. and it is only 1ns/day.... here is the script I used for
> submitting jobs:
>
> # @ job_name = gmx_test
> # @ class = kdm-large
> # @ error = gmx_test.err
> # @ output = gmx_test.out
> # @ wall_clock_limit = 00:20:00
> # @ job_type = bluegene
> # @ bg_size = 32
> # @ queue
> mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes
> -v -s npt
> _01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt" -mode
> VN -np 128
>
>
>
> here is my npt.mdp
>
> title                    = NPT-01
> cpp                      = /usr/bin/cpp
> include                  =
> define         = -DPOSRES  -DPOSRES_POPE_HEAD
> integrator               = md
> dt                       = 0.001
> nsteps                   = 5000000
> nstxout                  = 100000
> nstvout                  = 100000
> nstlog                   = 100000
> nstenergy                = 50000
> nstxtcout                = 50000
> xtc_grps                 =
> energygrps         = Protein SOL ION
> nstcalcenergy            = 10
> nstlist                  = 10
> nstcomm                  = 10
> comm_mode                = Linear
> comm-grps                = Protein_POPE    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         = 6
> DispCorr             = no
> tcoupl                   = V-rescale ;nose-hoover
> nhchainlength            = 1
> tc-grps                  = Protein_POPE    Water_and_ions
> tau_t                    = 0.1           0.1
> ref_t                    = 310         310
> Pcoupl                   = berendsen    ;parrinello-rahman
> Pcoupltype               = semiisotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5       4.5e-5
> ref_p                    = 1.0          1.0
> pbc             = xyz
> refcoord_scaling     = com
> gen_vel                  = no
> optimize_fft         = no
> constraints              = hbonds
> constraint_algorithm     = Lincs
>
> Does anybody have any advices?

Albert -

What is the speed using serial gromacs for the same system?


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA