Hi Ross, Dave,and Pratul,
Thank you all for the quick responses. I truly appreciate it.
I have double checked with the vendor and it seems they have tested the
overheating issue. I am planing on getting something similar to the link (
https://www.supermicro.com/products/system/4U/4029/SYS-4029GP-TRT2.cfm).
There is also an option of updating from the 92 GB RAM to the 192GB RAM for
about $1060. I guess the size of the RAM becomes increasingly important as
the size of the system increases?
Thank you for the tips on the CPU -- I actually have a related question.
Part of my research is to develop enhanced sampling method and I have been
using Plumed (
http://www.plumed.org/). As far as I know, Plumed have been
tested and patched with AMBER 14. Could you please comment on the
compatibility of Plumed with AMBER18?
Thanks again for your help.
Rui
*Rui Sun*
Assistant Professor
Department of Chemistry
University of Hawaii at Manoa
Bilger 245B
2545 McCarthy Mall
Honolulu, HI 96822-2275
Phone: (808) 956-3207
On Mon, Dec 17, 2018 at 5:38 PM David Cerutti <dscerutti.gmail.com> wrote:
> Thanks to Ross and Pratul for helping out here. I'll just emphasize that
> Amber's GPU code is really insensitive to the CPU. The speed of that
> processor affects less than 1% of the calculation, so any CPU core will be
> able to handle the communications and kernel launches. The only exceptions
> would be if you are doing special cases of GaMD or NEB which involve hybrid
> CPU / GPU calculations, in which case your run speed will be partly
> dependent on the speed of the CPU.
>
> I'll post more to the list as the story of my 300W RTX cards develops.
>
> Dave
>
>
> On Mon, Dec 17, 2018 at 8:55 PM Ross Walker <ross.rosswalker.co.uk> wrote:
>
> > Hi Rui,
> >
> > Note Gold 5115 CPUs are overkill for GPU AMBER unless you also plan to
> run
> > a lot of CPU based calculations. You can likely back this off to Silver
> > 4114 CPUs and save yourself about $1400 or a so a node.
> >
> > In terms of the GPUs either option is good assuming the vendor supplying
> > them is properly testing them to make sure they give correct numerical
> > results and that the cooling is sufficient that the cards do not thottle
> > during benchmarking. You can use the Amber benchmark suite from the GPU
> > page to test this. That will run in each GPU in turn and then on all GPUs
> > at once. In both cases you should see identical performance for all GPUs
> > whether they are being used individually or all at the same time. Note to
> > achieve this with RTX2080TI in 4x or 8x configs, where there is not space
> > between the GPUs required developing a custom cooling solution. This is
> > what Exxact had to do for their AMBER systems (
> > https://www.exxactcorp.com/AMBER-Certified-MD-Systems <
> > https://www.exxactcorp.com/AMBER-Certified-MD-Systems>) so if you are
> > using a different vendor you should ask them what their cooling solution
> > is, what the card base model they are using is, and if they can guarantee
> > there won't be throttling due to heat.
> >
> > Note if the 4 GPU system is really a 4.5U 8 GPU box with GPUs spaced by 2
> > PCI slots in each case then you should be okay but if it is a 2U x 4GPU
> box
> > you will have the same issues as the 8 GPU system.
> >
> > Hope that helps. Let me know if you want help speccing anything up
> further
> > - disk, memory etc.
> >
> > All the best
> > Ross
> >
> > > On Dec 17, 2018, at 19:46, Rui Sun <ruisun.hawaii.edu> wrote:
> > >
> > > Thank you for the quick response, Dave.
> > >
> > > If I may bother you with another question, the options that I have
> right
> > > now are:
> > > #1: *4* units of RTX 2080 + 2 units of Intel Gold 5115 per node
> ($16,000)
> > > #2: *8* units of RTX 2080 + 2 units of Intel Gold 5115 per node
> ($26,000)
> > >
> > > Apparently, the 8-unit node will be more cost-effective but do you
> think
> > I
> > > might have a cooling issue?
> > >
> > > Best,
> > > Rui
> > >
> > >
> > > *Rui Sun*
> > > Assistant Professor
> > > Department of Chemistry
> > > University of Hawaii at Manoa
> > > Bilger 245B
> > > 2545 McCarthy Mall
> > > Honolulu, HI 96822-2275
> > > Phone: (808) 956-3207
> > >
> > >
> > > On Fri, Dec 14, 2018 at 1:13 PM David Cerutti <dscerutti.gmail.com>
> > wrote:
> > >
> > >> The RTX-2080Ti is performing very well, but be careful about the
> > cooling!
> > >> I want to release a patch and I know what fixes to make, but I still
> > don't
> > >> have a good test platform as the card in my new workstation is getting
> > up
> > >> to 88*C (it'll shut down for safety purposes at 89). The card is also
> > not
> > >> putting out the performance that RTX-2080Tis in Ross's machines, which
> > seem
> > >> to have better cooling, are able to do. This is a 300W card--and
> while
> > 300
> > >> versus 250W may not seem like a big deal consider the excess heating
> in
> > a
> > >> confined volume of the same size inside a system of the same size with
> > the
> > >> same fans. About like you if you started eating two extra candy bars
> a
> > >> day--the calories would add up fast. So the benchmark numbers on the
> > >> website are genuine, and the GB portion may even come up to speed with
> > >> Volta more once we retune those kernels for Turing, but understand
> that
> > >> this horse needs lots of water.
> > >>
> > >> Dave
> > >>
> > >>
> > >> On Fri, Dec 14, 2018 at 5:54 PM Rui Sun <ruisun.hawaii.edu> wrote:
> > >>
> > >>> Dear AMBER Users,
> > >>>
> > >>> I was wondering if I could get some information on the performance of
> > >>> AMBER18 on the recently-released RTX 2080Ti. How is it comparing to
> > Titan
> > >>> V?
> > >>>
> > >>> Currently, I am considering buying a few GPU nodes and I am currently
> > >>> debating between the following two configurations:
> > >>> #1: 4 units of Titan V + 2 units of Intel Gold 5115 per node
> > >>> #2: 8 units of RTX 2080 + 2 units of Intel Gold 5115 per node
> > >>>
> > >>> Thank you so much,
> > >>> Rui
> > >>>
> > >>>
> > >>> *Rui Sun*
> > >>> Assistant Professor
> > >>> Department of Chemistry
> > >>> University of Hawaii at Manoa
> > >>> Bilger 245B
> > >>> 2545 McCarthy Mall
> > >>> Honolulu, HI 96822-2275
> > >>> Phone: (808) 956-3207
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 18 2018 - 03:00:03 PST
