[gmx-users] Gromacs parellal run:: getting difference in two trajectories

vivek sharma viveksharma.iitb at gmail.com
Fri Sep 12 09:26:17 CEST 2008 

Hi Carsten,
Thanks for your reply. Actually I am running MD simulation on a protein
molecule with 270 residues(2687 atoms), after adding water it is having
45599 atoms, and using the recent version of gromacs test available from
gromacs.org (gmxtest-3.3.3.tgz)
Following are the entries from the .mdp file I am using.....

**********md.mdp
title               = trp_drg MD
cpp                 = /lib/cpp ; location of cpp on SGI
constraints         = all-bonds
integrator          = md
dt                  = 0.002 ; ps !
nsteps              = 25000 ; total 50 ps.
nstcomm             = 1
nstxout             = 2500 ; output coordinates every 5.0 ps
nstvout             = 0
nstfout             = 0
nstlist             = 5
ns_type             = grid
rlist               = 0.9
coulombtype         = PME
rcoulomb            = 0.9
rvdw                = 1.4
fourierspacing      = 0.12
fourier_nx        = 0
fourier_ny        = 0
fourier_nz        = 0
pme_order         = 6
ewald_rtol        = 1e-5
optimize_fft      = yes
; Berendsen temperature coupling is on in four groups
Tcoupl                = berendsen
tau_t                 = 0.1         0.1   0.1
tc-grps               = protein     NDP   sol
ref_t                 = 300         300   300
; Pressure coupling is on
Pcoupl              = berendsen
pcoupltype          = isotropic
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529



****************and Following are the commands I am using
grompp_d -np 128 -f md1.mdp -c 1XU9_A_b4em.gro -p 1XU9_A.top -o
1XU9_A_md1_np128.tpr

submit
mdrun_d
/////arguement for mdrun_d
-s 1XU9_A_md1_np128.tpr -o 1XU9_A_md1_np128.trr -c 1XU9_A_pmd1_np128.gro -g
md_np128.log -e md_np128.edr -np 128

***********Following is the error I am getting
Reading file 1XU9_A_md1_np128.tpr, VERSION 3.3.3 (double precision)
starting mdrun 'CORTICOSTEROID 11-BETA-DEHYDROGENASE, ISOZYME 1'
25000 steps,     50.0 ps.

srun: error: n141: task1: Segmentation fault
srun: Terminating job

****************************************************************
Is this information is helpfull in figuring out the problem.
Please, advice

With Thanks,
Vivek

2008/9/11 Carsten Kutzner <ckutzne at gwdg.de>

> vivek sharma wrote:
>
>> Hi There,
>> I am running gromacs parellal version on cluster, with different -np
>> options.
>>
> Hi,
>
> which version of gromacs exactly are you using?




>
>
>  On analyzing the 5 nsec trajectory using ngmx, I am finding difference in
>> the trajectory of two similar runs (only thing varying in two runs in -np
>> i.e 20 and 64 ), where mdp file and input files are same in two cases.
>> I am wondering why I am getting this difference in two trajectories ?
>> I am looking for the advice whether I did something wrong or what may be
>> the probable reason for this difference.
>>
>
> There are many reasons why a parallel run does not yield binary identical
> results to a run with another number of processors, even if you start from
> the same tpr file. If you use PME, then the FFTW could pick a slightly
> different algorithm (it will select the fastest for that number of
> processors.
> This feature you can turn off by passing --disable-fftw-measure to the
> gromacs configure script). But still you can get results that are not
> binary identical if you do FFTs on a varying number of CPUs. Also, for
> limited accuracy which is inherent to any computer, additions need not
> be associative, which can show up in parallel additions.
>
> Generally, if you run in double precision, these effects will be way
> smaller,
> but nevertheless you won't get binary identical results. This will in all
> cases lead to trajectories which slowly diverge from each other. However,
> in the fist few hundred time steps, you should not see any difference in
> the first couple of decimals of the variables (positions, velocities,
> energies ...)
>
>  Also, I am not able to run gromacs faster by increasing the -np issue,
>>
>
> Please provide the exact command line you used.
>
>  Is there any max limit for scaling gromacs on parellal cluster ?
>>
>
> Yes, depending on your MD system and on the cluster you use :)
>
> Carsten
>
>
>  With Thanks,
>> Vivek
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics Department
> Am Fassberg 11
> 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/research/dep/grubmueller/
> http://www.gwdg.de/~ckutzne <http://www.gwdg.de/%7Eckutzne>
>
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