[gmx-users] some hardware questions

Peter C. Lai pcl at uab.edu
Wed May 2 17:44:58 CEST 2012

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.

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.

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.

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)

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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