[gmx-users] hyperthreading

[chris.neale at utoronto.ca]

I haven't tried mdrun -nt based hyperthreading, but I have tested  
using -np 16 on an 8 core box. I get an 8% to 18% performance increase  
when using -np 16 and optimizing -npme as compared to -np 8 and  
optimizing -npme. This is on a cluster of Intel Xeon E5540 aka  
"Nehalem" with 2 quad cores in a single box and using gromacs 4.0.7. I  
now regularly overload the number of processes.

selected examples:
System A with 250,000 atoms:
mdrun -np 8  -npme -1    1.15 ns/day
mdrun -np 8  -npme  2    1.02 ns/day
mdrun -np 16 -npme  2    0.99 ns/day
mdrun -np 16 -npme  4    1.36 ns/day <-- 118 % performance vs 1.15 ns/day
mdrun -np 15 -npme  3    1.32 ns/day

System B with 35,000 atoms (4 fs timestep):
mdrun -np 8  -npme -1    22.66 ns/day
mdrun -np 8  -npme  2    23.06 ns/day
mdrun -np 16 -npme -1    22.69 ns/day
mdrun -np 16 -npme  4    24.90 ns/day <-- 108 % performance vs 23.06 ns/day
mdrun -np 56 -npme 16    14.15 ns/day

Cutoffs and timesteps differ between these runs, but both use PME and  
explicit water.

I'd be interested in hearing about any comparisons between -np based  
process overloading and -nt based hyperthreading.

Hope it helps,
Chris.

-- original message --

Hi,

These are nehalem Xeons I presume?
Then you get 15 to 20% more performance in Gromacs running 2 vs 1  
thread or process per physical core.

Berk

> Date: Fri, 6 Aug 2010 09:24:11 -0500
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] hyperthreading
>
> Dear All,
>
> I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
> uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
> roughly 16 GB of RAM each.
>
> In any case, I wanted to inquire about hyperthreading. Does anyone
> have experience on similar machines with vs. without hyperthreading?
> The ROCKS users list suggests that hyperthreading ought always be off
> for HPC applications, which sounds overly simplistic to me, though I
> more or less follow the logic of this.
>
> So, has anyone done any benchmarking yet in a similar setting, and
> what thoughts do you have? I obviously can do some benchmarking myself
> as well but I thought I'd check in with the list first.
>
> Thanks so much,
> David
>
>
> -- 
> David Mobley
> dmobley at gmail.com
> 504-383-3662