An update:<br>Using a 4th order PME spline resulted in ~ 15 % increase in efficiency. <br><br>Thank you, Carsten.<br><br><div class="gmail_quote">On Mon, Mar 24, 2008 at 3:08 PM, maria goranovic <<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear All,<br><br>My apologies. I had too big a simulation cell, and too few atoms, hence the problem.<br>
<br>No particular reason to choose order 5. I will try with pme_order 4 and see if it improves performance anyway.<br>
<br>thanks ! <br><font color="#888888"><br>-maria</font><div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Mon, Mar 24, 2008 at 2:19 PM, Carsten Kutzner <<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Am 24.03.2008 um 10:17 schrieb maria goranovic:<br>
<div><br>
> Hi Folks,<br>
><br>
> My simulation is running too slow. It took 10 wall clock hours (40<br>
> cpu hours) for a short 50 ps simulation of a ~ 23000 atom DPPC<br>
> bilayer. The hardware is a 4-cpu core. The installation is gromacs<br>
> 3.3.1. I have run much larger systems (~ 160000 atoms) using the<br>
> same gromacs installation on the same hardware, and they run much<br>
> faster than this (200 ps per 40 cpu hours).<br>
><br>
> Can anybody suggest why this is happening ? Is it because of latency<br>
> in the cpu communication? If so, what is the workaround ?<br>
</div>Is there a special reason for using pme_order=5? I would use the<br>
default, 4 instead, or at least an even number.<br>
<br>
Carsten<br>
<div><div></div><div><br>
> My .mdp script is below.<br>
> These are the run commands.<br>
><br>
> grompp -np 4 -v -f heat.mdp -c minim4.gro -p dppc.top -n dppc.ndx -o<br>
> heat.tpr<br>
> mpirun -np 4 ~/bin/mdrun_mpi -np 4 -v -s heat.tpr -o heat.trr -c<br>
> heat.gro -e heat -g heat.log > & heat.out<br>
><br>
> ;###########################################<br>
> ; heat.mdp<br>
> ;<br>
> title = heating<br>
> cpp = /usr/bin/cpp<br>
> constraints = hbonds<br>
> constraint_algorithm = lincs<br>
> unconstrained_start = yes<br>
> integrator = md<br>
> nsteps = 25000<br>
> dt = 0.002<br>
> comm_mode = linear<br>
> nstxout = 5000<br>
> nstvout = 5000<br>
> nstlog = 5000<br>
> nstenergy = 5000<br>
> nstlist = 10<br>
> ns_type = grid<br>
> pbc = xyz<br>
> ; ------------------<br>
> coulombtype = PME<br>
> rcoulomb = 1.0<br>
> vdwtype = cut-off<br>
> rlist = 1.0<br>
> rvdw = 1.0<br>
> fourierspacing = 0.1<br>
> pme_order = 5<br>
> ewald_rtol = 1e-5<br>
> ; ---------------------------<br>
> ; Berendsen temperature and preasure coupling<br>
> Tcoupl = berendsen<br>
> tc-grps = DPPC SOL<br>
> tau_t = 0.6 0.6<br>
> ; i have also tried a tau value of 0.1, but no speed up<br>
> ref_t = 323.0 323.0<br>
> Pcoupl = berendsen<br>
> Pcoupltype = semiisotropic<br>
> tau_p = 1.0 1.0<br>
> compressibility = 4.5e-5 4.5e-5<br>
> ref_p = 1.0 1.0<br>
> ; ---------------------------<br>
> gen_vel = yes<br>
> gen_temp = 323.0<br>
> gen_seed = 194040<br>
> ;###########################################<br>
><br>
> --<br>
> Maria G.<br>
> Technical University of Denmark<br>
</div></div>> Copenhagen _______________________________________________<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen