[gmx-users] AMD vs Intel, nvidia 20xx

Tamas Hegedus tamas at hegelab.org
Wed Sep 19 10:58:08 CEST 2018


I am planning to buy 1 or 2 GPU workstations/servers for stand alone 
gromacs and gromacs+plumed (w plumed I can efficiently use only 1 GPU). 
I would like to get some suggestions for the best performance/price 
ratio. More specifically, some info on the correlation between PCI lines 
and performance.

Based on google, gmx mail list, and my experience I think that
* i9 with 44PCI lines
* 4 gtx 1080Ti
are OK and fits the budget.

However, there are several upcoming issues:

1. I expect the 4 GPUs running at 70% (1PME and 3PP) with 16 cores. I do 
not know if the 44PCI lines are limiting or not?

2. 4x8 channel are OK? Should I look for a mother board with a PLX chip 
that makes 64 virtual pci lines? Do you have experience with this type 
of mobo? I have red that the average will be better than 4x8, but others 
say that its makes the system slower.

3. An option might be go with AMD CPUs with higher PCI line, but I do 
not trust AMD when high CPU performance is needed. But this might come 
from the past and I should forget this. Have you used recent AMD 
processors with gromacs with GPU acceleration?

4. I have the feeling using gmx 2018 that I would not gain performance 
with (physical) 32 cores and 4 GPUs, since 16 already is sufficient and 
the 70% GPU usage is not because waiting for the CPU. I do not know 
about this (how to check this). What is your experience?

5. I am afraid to buy more GPU power than necessary.
It might be better to buy 2 faster and 2 slower GPU or only 3 newer GPUs 
to optimize the system.
However, I most likely can not get 1070Ti. In addition, is better for 
the system not to run at 100%.
BUT: there will be new RTX 20xx out and likely I can get lower version 
number for less power consumption and the same computing capacity (e.g. 
2070 instead of 1080).
BUT: it seems for me that RTX2070 has much less cores (2304) than 1080Ti 
and 2080Ti has more cores than 1080Ti.
1080, 4*3584 cores, 64 PCI lines
2080, 3*4352 cores, 48 PCI lines
However, in the letter case more PP may run on the GPU and again the 
CPU/GPU communication may become the limiting factor.

Thanks for all the opinion and suggestion,

Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University     | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47        | mailto:tamas at hegelab.org
Budapest, 1094, Hungary   | http://www.hegelab.org

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