[gmx-users] some hardware questions

[Szilárd Páll]

On Wed, May 2, 2012 at 11:51 AM, 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.

I can't comment on Ivy bridge, but when it comes to Sandy Bridge, with
the new NxX non-bonded kernels this is roughly the performance you
should expect:
- an FX-8150 should have a performance close to the SB i7-2600 (with
PME I've seen up to 10-15% advantage to the AMD)
- an SB-E will have slightly higher per core performance than SB, e.g.
in the benchmark I've done an i7-3930K was 1.6x faster than SB i7-2600
even though the latter has higher stock frequency.

> 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).

Not even OpenMP 3.1 supports GPUs. We will be considering OpenCL
support in the future and with it support for AMD GPUs, but don't
expect it anytime soon. However, rest assured that as soon as AMD GPUs
become more widely adopted on HPC, GROMACS will make use of them.

> 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.

There are differences mostly when it comes to latency and reliability,
but I can't quantify it. However, instead of struggling with 1 Gb
ehternet you might want to consider sticking to single-node runs using
say a dual 16-core Interlagos setup.

Cheers,
Szilárd

> Thanks a lot.
>
> Milan Melichercik
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