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 <[EMAIL PROTECTED]> > 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > 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> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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