[gmx-users] some hardware questions
szilard.pall at cbr.su.se
Mon May 7 23:56:45 CEST 2012
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
> 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
> 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
> 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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