[gmx-users] Gromacs parellal run:: getting difference in two trajectories
viveksharma.iitb at gmail.com
Fri Sep 12 09:26:17 CEST 2008
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
Following are the entries from the .mdp file I am using.....
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
/////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.
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
> 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
> 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
> 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 :)
> With Thanks,
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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.gwdg.de/~ckutzne <http://www.gwdg.de/%7Eckutzne>
> gmx-users mailing list gmx-users at gromacs.org
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