[gmx-users] some hardware questions

[Szilárd Páll]

On Wed, May 2, 2012 at 5:44 PM, Peter C. Lai <pcl at uab.edu> wrote:

> When considering compute hardware today, you're gonna have to shop like a
> gamer. A rig that can get high Battlefield 3 or Arma 2/3 framerates should
> also be able to get you some nice ns/day.
>

(To a great extent) wong! While many if not most games are GPU-bound and
not well multi-threaded, GROMACS uses highly efficient CPU code and can
make use of virtually any amount of CPU juice (i.e. extra cores and
frequency).


> I think most people consider Bulldozer mostly a flop. AMD masks lower
> cycle speeds with more cores per chip, but that just shifts the burden onto
> interprocessor communication, to which MPI is the most sensitive.
>

Partly true, but GROMACS has no issues whatsoever with scaling pretty much
linearly to any number of cores currently available per node  (with at
least 500 atoms/core).


> You can wait for ivy bridge, then stick some Kepler GPUs (nvidia gtx 680)
> in it. That should max the performance. asm is pretty much stagnant for
> general purpose procs since core2 came out.
>

AFAIK IB doesn't improve much on flop/s performance over SB, but it's a
power efficiency king. However, it's not at all sure that when it comes to
performance/$ AMD doesn't win. Also, Kepler might not be the best choice,
we'll see what can we get out with some more tuning.

What do you mean by asm?


> Keep an eye on the I7-3770K. It has the most cache and fastest core speed
> of the intel ones. The K chips are preferred for adventurous overclocking.
> Although hyperthreading and onboard intel gpu is useless for hpc. The
> I5-3570K is slower and has 2M less cache - it's basically an ivy bridge
> drop in replacement for the I5-2500K (just pci-e 3.0 upgrade)
>

Ehmm, HT *is* useful, it will boost GROMACS performance by up to 10-15% or
so.


> gmx 4.6 is supposed come with native gpu support; you should look at some
> list archives to see what is planned to be supported. Waiting for 4.6 to
> come out is going to extend your wait on hardware considerations, but it
> also means prices should drop.
>
> for nics find the best/most compatible tcp offloading engine, also while
> using jumbo frames. Personally I've always found Intel better than
> Broadcom. Stay away from anything Realtek. If you can, try to begin to look
> at going to fiber earlier (with an eye on splitting out storage from
> compute).
> --
> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
>
>
> melichercik <melichercik at nh.cas.cz> wrote:
>>
>> Hi people,
>> we plan to buy some computer mostly for gromacs, so I want to ask you
>> for some hints. I'd tried to do some research, but no success. :(
>>
>> Have someone ever compared AMD Bulldozer and Sandy/Ivy Bridge
>> architectures? Are there planed any optimizations in gmx core in asm
>> parts? (if there are need).
>> Most interesting for me whould be to compare FX-8150 and i5-2550,
>> I7-2600, i7-3570K or i7-3770 processors.
>>
>> GPGPU - are there some real plans for supporting Radeon GPUs? Because
>> OpenMP 3.x supports them - but I don't have any idea how complicate is
>> to use newer OpenMP in GMX (and another work about it).
>>
>> And are there bigger differences (if someone knows) in use 1 Gbps
>> onboard NIC vs. "better"? add-on NIC cards e.g. Intel Pro/1000 CT or
>> similar? In MPI calculations with use 4 to 8 cores per computing node.
>>
>>
>> Thanks a lot.
>>
>> Milan Melichercik
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