<div dir="ltr">Hi Carsten,<br>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 <a href="http://gromacs.org">gromacs.org</a> (gmxtest-3.3.3.tgz)<br>
Following are the entries from the .mdp file I am using.....<br><br>**********md.mdp<br>title = trp_drg MD<br>cpp = /lib/cpp ; location of cpp on SGI<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 25000 ; total 50 ps.<br>nstcomm = 1<br>nstxout = 2500 ; output coordinates every 5.0 ps<br>nstvout = 0<br>nstfout = 0<br>
nstlist = 5<br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 1.4<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in four groups<br>Tcoupl = berendsen<br>
tau_t = 0.1 0.1 0.1 <br>tc-grps = protein NDP sol <br>ref_t = 300 300 300 <br>; Pressure coupling is on<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>
tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
<br><br><br>****************and Following are the commands I am using<br>grompp_d -np 128 -f md1.mdp -c 1XU9_A_b4em.gro -p 1XU9_A.top -o 1XU9_A_md1_np128.tpr<br><br>submit<br>mdrun_d<br>/////arguement for mdrun_d<br>-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<br>
<br>***********Following is the error I am getting<br>Reading file 1XU9_A_md1_np128.tpr, VERSION 3.3.3 (double precision)<br>starting mdrun 'CORTICOSTEROID 11-BETA-DEHYDROGENASE, ISOZYME 1'<br>25000 steps, 50.0 ps.<br>
<br>srun: error: n141: task1: Segmentation fault<br>srun: Terminating job<br><br>****************************************************************<br>Is this information is helpfull in figuring out the problem.<br>Please, advice <br>
<br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">2008/9/11 Carsten Kutzner <span dir="ltr"><<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi There,<br>
I am running gromacs parellal version on cluster, with different -np options.<br>
</blockquote></div>
Hi,<br>
<br>
which version of gromacs exactly are you using?</blockquote><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
I am wondering why I am getting this difference in two trajectories ?<br>
I am looking for the advice whether I did something wrong or what may be the probable reason for this difference.<br>
</blockquote>
<br></div>
There are many reasons why a parallel run does not yield binary identical<br>
results to a run with another number of processors, even if you start from<br>
the same tpr file. If you use PME, then the FFTW could pick a slightly<br>
different algorithm (it will select the fastest for that number of processors.<br>
This feature you can turn off by passing --disable-fftw-measure to the<br>
gromacs configure script). But still you can get results that are not<br>
binary identical if you do FFTs on a varying number of CPUs. Also, for<br>
limited accuracy which is inherent to any computer, additions need not<br>
be associative, which can show up in parallel additions.<br>
<br>
Generally, if you run in double precision, these effects will be way smaller,<br>
but nevertheless you won't get binary identical results. This will in all<br>
cases lead to trajectories which slowly diverge from each other. However,<br>
in the fist few hundred time steps, you should not see any difference in<br>
the first couple of decimals of the variables (positions, velocities,<br>
energies ...)<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also, I am not able to run gromacs faster by increasing the -np issue, <br>
</blockquote>
<br></div>
Please provide the exact command line you used.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Is there any max limit for scaling gromacs on parellal cluster ?<br>
</blockquote>
<br></div>
Yes, depending on your MD system and on the cluster you use :)<br>
<br>
Carsten<div class="Ih2E3d"><br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
With Thanks,<br>
Vivek<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
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<br>
-- <br></div>
Dr. Carsten Kutzner<br>
Max Planck Institute for Biophysical Chemistry<br>
Theoretical and Computational Biophysics Department<br>
Am Fassberg 11<br>
37077 Goettingen, Germany<br>
Tel. +49-551-2012313, Fax: +49-551-2012302<br>
<a href="http://www.mpibpc.mpg.de/research/dep/grubmueller/" target="_blank">http://www.mpibpc.mpg.de/research/dep/grubmueller/</a><br>
<a href="http://www.gwdg.de/%7Eckutzne" target="_blank">http://www.gwdg.de/~ckutzne</a><div><div></div><div class="Wj3C7c"><br>
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