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

[Albert]

hello guys:

    thank you very much for kind reply.

    I am not sure about the thread version since there is only bigsize 
version of it. And the administrator told me that I have to use the 
multiples of 32 in the bg_size parameter. The number specified in "-np" 
should be 4 times bg_size.
   Probably I should compile it by myself. Does anybody have any idea 
how to compile gromacs in blue gene?

thank you very much
Albert



On 04/25/2012 12:31 AM, Dr. Vitaly V. Chaban wrote:
>> 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