[gmx-users] Gromacs parellal run:: getting difference in two trajectories
vivek sharma
viveksharma.iitb at gmail.com
Fri Sep 12 09:28:09 CEST 2008
Sorry, I forgot to mention that one cofactor NDP, I added in my molecule
using PRODRG server.
2008/9/12 vivek sharma <viveksharma.iitb at gmail.com>
> 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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>
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