[3dem] Single GPU workstation

[Takanori Nakane]

Hi,

 > how much Relion still profits from AVX512

AVX 512 is very beneficial for CPU-based motion correction.
The advantage mostly comes from Intel MKLFFT.

Unfortunately (but understandably), MKLFFT does not run very fast on AMD CPUs,
so I'm not sure if AVX 512 on AMD CPUs is actually useful for RELION's
motion correction.

Also note that Zen 4's SIMD units are only 256 bit wide. AVX 512 needs
two cycles. Thus, AVX 512 on Zen 4 does not improve throughput over
AVX 256.

Best regards,

Takanori Nakane

On 2022/11/21 20:54, Kilian Schnelle wrote:
> I may would think about a Zen-4 CPU like the 7950X. I don’t know how much Relion still profits from AVX512 but sadly Intel decided to disable that on 
> the 13900K, the new AMDs support it now. Also the AMD has 4 more PCIe lanes, which may come in handy if you want more NVMe SSDs or update later to a 
> second GPU. Though it only has DDR5 support which will cost more.
> 
> Apart from that air cooling is just as good, if not sometimes better, then AIO, and you need a good airflow in the case for the GPU anyway if u don’t 
> plan to upgrade that also to a water block. Would recommend the good old Noctua fans.
> 
> For the GPU you may even get 2 older generation ones for the price of one 4090, so not sure its worth it (someone has benchmarks already?), also be 
> sure to seat the power cable correctly/ check after delivery, could get crispy else ;)
> 
> Cheers
> Kilian
> 
> Kilian Schnelle
> Department of Structural Biology
> University of Osnabrueck
> Barbarastr. 13
> D-49076 Osnabrueck, Germany
> Phone: +49 541 969 7508
> Email: kilian.schnelle at uni-osnabrueck.de
> 
> 
> 
> 
>> On 17. Nov 2022, at 13:25, Kovtun, Oleksiy <oleksiy.kovtun at mpinat.mpg.de> wrote:
>>
>> Dear all,
>>
>> I am configuring mid-performance systems for SPA and STA processing.
>> Systems are aimed at testing processing parameters and processing small to medium datasets in frugal box sizes. They will be installed in an office 
>> and serve as individual workstations.
>> Currently, I come down to the following:
>> i9-13900k AIO cooling, 128GB DDR4-3200, 4TB SSD scratch, 10GB LAN.
>> For the GPU, I consider 24GB cards:
>> RTX 3090 -  the basic choice.
>> RTX 3090ti - much extra heat for nothing, but surprisingly more available than 3090.
>> RTX4090 - will this perform better in RELION? Extra CUDA cores, but the same VRAM size and bandwidth as 3090. It may run cooler and quieter, though. 
>> Has anyone had a successful installation, and RELION runs on it?
>> RTX A5000 - a step price overhead for overheating insurance. It may be a necessary evil for an office-based PC.
>>
>> Please let me know what option will be better and whether the core system configuration ( is BIG.Little of i9 a problem? ) looks adequate.
>>
>> Thank you and best,
>>
>> Oleksiy
>>
>>
>> -----------------------------------------------------
>> /*Dr Oleksiy Kovtun
>> *Max-Planck Research Group Leader
>> Molecular Mechanisms of Membrane Trafficking
>> Max-Planck-Institute for Multidisciplinary Sciences
>> City-Campus, Hermann-Rein-Str. 3, 37075 Göttingen
>> Germany
>> Email: oleksiy.kovtun at mpinat.mpg.de <mailto:oleksiy.kovtun at mpinat.mpg.de>/
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