[gmx-users] Hardware for GROMACS

[Szilárd Páll]

Raman,

First, please please have a look at the documentation and check out the
relevant GROMACS papers (http://www.gromacs.org/Gromacs_papers), in
particular http://dx.doi.org/10.1002/jcc.24030

On Tue, Jul 4, 2017 at 5:56 PM, Raman Preet Singh <
ramanpreetsingh at hotmail.com> wrote:

> Hello,
>
>
> I am new to GROMACS and want to assemble a computer to run simulations of
> proteins and polymers (typically <50 kD). My questions are:
>
> 1. I plan to add two or three small-sized GPUs (768 CUDA cores/GPU) to the
> system. Is it OK to have a dual core processor or should I look for a
> processor with 6 or 8 cores?
>

Look at publised benchmark and performance analysis in the above paper to
familiar with the resource requirements of GROMACS.

Briefly: current releases require balanced CPU-GPU resources; depending ion
your hardware, type of system, and simulation you intend to run you'll
typically need 4-6 desktop CPU cores (and 8+ server) per GPU for balanced
runs.

This will slightly change in a coming release, but even than you'll
typically want at least 2 fast or 4-6 slow cores/GPU.

Depending on what type of/how many concurrent runs you want to execute,
several small GPUs might (actually, will often) not be the ideal setup. Get
fewer but faster GPUs (e.g. 2x GTX 1070 instead of 3x 1050), especially if
you don't want to run many concurrent jobs.


> 2. GROMACS website (http://www.gromacs.org/GPU_acceleration) has a page
> on GPU acceleration and compares performance between different hardware
> combinations (6 core or 2*8 cores, with and without GPUs). It also mentions
> of "dodec + vsites(5fs)". I tried searching on Google but could not find
> what is "dodec+vsites(5fs)". Please help me understand these.
>

Please read the literature.
Briefly:
- dodec:
https://image.slidesharecdn.com/gromacs-kepler-gpus-gtc-express-webinar-140121150157-phpapp01/95/gromacs-and-kepler-gpus-12-638.jpg?cb=1390318156
- vsites:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html


> 3. Apart from a good processor and 2-3 GPUs, is there any other hardware
> that I may require to accelerate the calculations. I am targeting
> simulations in time scales of a few hundred nanoseconds.
>

You might need some disc space :) Memory not much at all (except for some
types of analyses).


>
> Thanks in advance for your help!
>
>
> Regards,
>
> Raman
>
>
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