[Beowulf] recommendations for cluster upgrades

Tiago Marques a28427 at ua.pt
Sun May 17 14:25:18 EDT 2009


On Sun, May 17, 2009 at 12:04 PM, Jan Heichler <jan.heichler at gmx.net> wrote:

>  Hallo Tiago,
>
>
> Sonntag, 17. Mai 2009, meintest Du:
>
>
>
>  On Sat, May 16, 2009 at 11:56 PM, Rahul Nabar <rpnabar at gmail.com> wrote:
>
>
> On Sat, May 16, 2009 at 2:34 PM, Tiago Marques <a28427 at ua.pt> wrote:
>
> > One of the codes, VASP, is very bandwidth limited and loves to run in a
>
> > number of cores multiple of 3. The 5400s are also very bandwith - memory
> and
>
> > FSB - limited which causes that they sometimes don't scale well above 6
>
> > cores. They are very fast per core, as someone mentioned, when compared
> to
>
> > AMD cores.
>
>
> Thanks Tiago. This is super useful info. VASP is one of our major
>
> "users" too. Possibly 40% of the cpu-time. Rest is a similar
>
> computational chemistry code, DACAPO.
>
>
> It would be interesting to compare my test-run times on our
>
> AMD-Opterons (Barcelona). Is is possible to share what your benchmark
>
> job was?
>
>
> I'll try to talk to the user who crafted it for me before, but it should be
> no problem to pass it to you after.
>
>
>
>
>
> Since you mention VASP is bandwidth limited do you mean memory
>
> bandwidth or the interconnect? Maybe this question itself is naiive.
>
> Not sure. What interconnect do you use? We have gigabit ethernet dual
>
> bonded.
>
>
> Memory bandwith, as you can see by the performance gain from going to
> 1600MHz from 1066, even with looser timings IIRC.
>
> Of course interconnects also play a role, even internal ones, which in the
> case of Xeons was a very slow FSB.
>
>
> I use single GbE because for as much as I could benchmark, I hardly found
> anything that could use more than one node efficiently and no one - not even
> here - could help me with that. Seems I need infiband.
>
> I only managed to increase 33% with two nodes when using a really huge
> job(+100k atoms) on Gromacs.
>
>
> For VASP you should look for ConnectX or InfiniPath. InfiniHost III scales
> badly for the scenarios i saw. It is probably because of the use of
> collectives.
>
> Ok, tks. I'll look into that for a future upgrade.


>
>
>   Which brings to a point that I forgot to mention to you. When
> considering Intel machines, you can always get a compiler license for $2000,
> give or take,
>
>
> 2000 USD sounds rather expensive. Node locked licenses are usually
> cheaper... Look for the package with Compilers, MKL and MPI - the Cluster
> Toolkit. Is definitely worth it (when buying more than just a single
> machine).
>
> It wasn't, Intel only required me that we purchase one license that can be
used to compile software for all nodes. Given the price of the 8 nodes, it
was a small percentage of the total. Still, it seems to be cheaper, I've
checked the Cluster Toolkit Compiler Edition for Linux costs $1699.
I mostly only use ICC, Ifort and sometimes MKL. Even MKL isn't faster than
GotoBLAS, although not by much, and I only use it when I need LAPACK
routines.
Best regards,
Tiago Marques


>
>
>
> Jan
>

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