[gmx-users] parallel problem
spoel at xray.bmc.uu.se
Wed Sep 3 23:17:01 CEST 2003
On Thu, 2003-09-04 at 01:52, Osmany Guirola Cruz wrote:
> No i have dual PIII 933MHz coupled by tcp/ip
> It is 100 Mbit
> My cluster have a switch i have 32 dual in a sub-net and only one
> machine is in my network (PBS)
> I do a simulation whit 9500 molecules of water (SOL) 129 proteins
> No i dont do the gromacs benchmarks , HOW COULD I DO IT?
Download them from gromacs.org...
I have done the test with a switched 100 Mbit/s network with dual 800
MHz P3s, up until 10 nodes (i.e. 20 cpus).
> i forget something , my simulations whith cutoff are shorter than PME
To efficiently use the dual processors you have to select another lam
option (rcp=usysv or rcp=sysv).
Now the real problem performancewise is PME. In the current 3.1.4
version PME does not behave well at all in parallel. On a Scali network
I use at most 4 dual Xeon nodes for my runs which have 30000 waters.
Since your system is smaller, performance will be even worse. Note that
the gromacs scaling benchmark is done with a (twin-range) cut-off rather
than PME. If you can live with a cut-off (and after all, the GROMOS96
force field was developed for use with a cut-off) you could maybe scale
to somewhat more processors:
nstlist = 5
rlist = 0.9
rcoulomb = 1.4
rvdw = 1.4
See how far you can go with that. Furthermore you want to control how
PBS/LAM allocates your processors. The communication is on a ring
topology in principle, so if you have two dual processor nodes
N0-p0, N0-p1, N1-p0, N1-p1
you want the jobs to be allocated in this order (to use the shared
memory communication) rather than
N0-p0, N1-p0, N0-p1, N1-p1
In the first example two of the four communications use shared memory,
in the other example none of them do.
> Really i need help, i have 32 machines and only use one for my
> simulations :-(
> David wrote:
> > On Wed, 2003-09-03 at 22:16, Osmany Guirola Cruz wrote:
> > > This is not the first time that i make the same question, how should i do gromacs work well whith lam in my linux cluster , a simulation in one machine is shorter than two machines , my last steep was compile the lammpi source whith the option tcp-short=524288 (512kb) and nothing happens .
> > >
> > > PLEASE HELPMEEEEEEEEEEEEEEEEEEEEEE
> > >
> > I'll just assume you have single processor machines coupled by tcp/ip
> > network, is that correct?
> > Is it 10 Mbit/s, 100 Mbit/s or better?
> > Do you have a switch between the machines or a hub?
> > How large is your system to simulate?
> > Did you try to reproduce the gromacs benchmarks?
> > >
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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