[gmx-users] 4 Titan X or 2?

[Szilárd Páll]

On Fri, May 22, 2015 at 4:37 PM, Kutzner, Carsten <ckutzne at gwdg.de> wrote:
>
>> On 22 May 2015, at 16:08, Albert <mailmd2011 at gmail.com> wrote:
>>
>> how about the following:
>>
>>
>> 2 x Intel Xeon E5­2680V3,12 cores, 2.5­3.3 GHz
> My guess is that two TITAN X will be more than enough to
> balance the CPU compute power. To save some money, you
> could also start with two GTX 980 instead of the TITANs
> and upgrade to four GTX 980 if you need more power on the
> GPU side.

That will likely be the case for AMBER runs with a short cut-off, but
with different ratio of short- to long-range work (or no long-range
work at all), the situation will change. E.g. with CHARMM using 1.2 nm
cut-off you'll have >2x more non-bonded work wrt 0.9 nm (!) and the
force switch modifier has a slight performance impact too.

I've just had a quick look and with a ~105k atom CHARMM membrane
protein a TITAN X gives about balanced simulation when combined with a
i7 5690X (8C @3-3.5 GHz). The 12-core E5-2680v3 is definitely faster
(even though this will not run at the base frequency of 2.5 Ghz but
rather at 2.1 GHz (2.9 max)), so with a CHARMM setup, and especially
with smaller systems a TITAN X may not be able to "keep up" with it an
E5-2680v3. You can still get two and upgrade to more later if
necessary.

Cheers,
--
Szilárd

For those interested in well-hidden actual clock frequencies of
Haswell Xeons (w and w/o AVX code), see page 10 of this rather hard to
find document:
http://www.intel.com/content/dam/www/public/us/en/documents/specification-updates/xeon-e5-v3-spec-update.pdf

> Carsten
>
>
>> Cool & Silent Features
>> Supermicro dual Xeon motherboard
>> 64GB ECC DDR4 RAM 4­channel 2133 MHz, 8 x 8 GB
>> 256GB Samsung SSD 850 PRO
>> 2 x 6000 GB WD Red hard drive, 7200 rpm
>> Asus GTX TITAN X, 12 GB GDDR5
>> Asus GTX TITAN X, 12 GB GDDR5
>> Asus GTX TITAN X, 12 GB GDDR5
>> Asus GTX TITAN X, 12 GB GDDR5
>> Supermicro Server tower / rack housing, 4 x GPU, 8 x hotswap bays
>> 2000W redundant power supply
>>
>>
>>
>>
>> On 05/22/2015 04:04 PM, Kutzner, Carsten wrote:
>>> That depends on what hardware you want to pair these with on the CPU side.
>>>
>>> Carsten
>>
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> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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