[gmx-users] Workstation choice

[Olga Selyutina]

Thank you, an idea to build own low-price cluster is very interesting.
Seven Ryzen 3 2200 with hardware cost ~$2000 and their total performance
for some purposes could be higher than performance of one high-performance
CPU with few GPUs (configurations CPU+GPUs mentioned in my previous letter)
. But I’m not sure that they provide higher performance for GROMACS
simulations.

2018-09-09 12:59 GMT+07:00 Benson Muite <benson.muite at ut.ee>:

> This is old, but seems to indicate Beowulf clusters work quite well:
>
> https://docs.uabgrid.uab.edu/wiki/Gromacs_Benchmark
>
> Szilárd had helped create a benchmark data set available at:
> http://www.gromacs.org/About_Gromacs/Benchmarks
> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
> ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz
>
> Does your use case involves a large number of ensemble simulations which
> can be done in single precision without error correction? If so might you
> be better building a small Beowulf cluster with lower spec processors that
> have integrated GPUs? For example a Ryzen 3 with integrated graphics is
> about $100. Motherboard, RAM, power supply would probably get you to about
> $300. Intel core I3 bundle would be about $350.  Setup could be done using
> OpenHPC stack:
> http://www.openhpc.community/
>
> This would get you a personal 5-7 node in house cluster. However, ability
> to do maintenance, have local support for repair may also be important in
> considering system lifetime cost, not just initial purchase price. Gromacs
> current and future support for OpenCl, and likely also important here.
>
> At least one computer store in my region has allowed benchmarking.
>
> On 09/07/2018 09:40 PM, Olga Selyutina wrote:
>
>> Hi,
>> A lot of thanks for valuable information.
>> If it isn’t difficult for you, could you answer how the growth of
>> performance under using the second GPU on the single simulation was
>> changed
>> in GROMACS 2018 vs older versions (2016, 5.1, it was 20-30% higher)?
>>
>>
>> 2018-09-07 23:25 GMT+07:00 Szilárd Páll <pall.szilard at gmail.com>:
>>
>> Are you intending to use it mostly/only for running simulations or also as
>>> a desktop computer?
>>>
>>> Yes, it will be mostly used for simulations.
>>>
>>
>> I'm not on the top of pricing details so you should probably look at some
>>> configs and get back with concrete CPU + GPU (+price) combinations and we
>>> might be able to guesstimate what's best.
>>>
>>>
>>> These sets of CPU and GPU are suitable for price (in our region):
>> *GPU*
>> GTX 1070 ~1700MHz, cuda 1920 - $514
>> GTX 1080 ~1700MHz, cuda 2560 - $615
>> GTX 1070Ti ~1700MHz, cuda 2432 - $615
>> GTX 1080Ti ~1600MHz, cuda 3584 - $930
>>
>> *CPU*
>> Ryzen 7 2700X - $357
>> 4200MHz, 8/16 cores/threads, cache L1/L2/L3 768KB/4MB/16MB, 105W, max.T
>> 85C
>>
>> Threadripper 1950X - $930
>> 4000MHz, 16/32 cores/threads, cache  L1/L2/L3 1.5/8/32MB, 180W, max.T 68C
>>
>> i7 8086K - $515
>> 4800MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C
>>
>> i7 8700K - $442
>> 4600MHz, 6/12 cores/threads, cache L2/L3 1.5/12MB, 95W, max.T 100C
>>
>> The most suitable combinations CPU+GPU are as follows:
>> 1) Ryzen 7 2700X + two GTX 1080 - $1587
>> 1.1) Ryzen 7 2700X + one GTX 1080 + one GTX 1080*Ti* - $1900 (maybe?)
>> 2) Threadripper 1950X + one GTX 1080Ti - $1860
>> 3) i7 8700K + two GTX 1080 - $1672
>> 4) Ryzen 7 2700X + three GTX 1070 - $1900
>> My suggestions:
>> Variant 1 seems to be the most suitable.
>> Variant 2 seems to be suitable only if the single simulation is running on
>> workstation
>> It’s a bit confusing that in synthetic tests/games performance of i7 8700
>> is higher than Ryzen 7 2700.
>> Thanks a lot again for your advice, it has already clarified a lot!
>>
>>
>>
>>
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-- 
С уважением, Ольга Селютина