I don't think $1060 for extra RAM will give you ROI. Main system memory is not a limitation in GPU runs and even most types of analyses. But you may have other programs that need it ...
I personally would go for extra storage, RAIDed disks, better network (even bonded multiple NICs) ...
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 12/18/2018 5:56 AM, Rui Sun wrote:
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><mailto: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><mailto: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><
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><mailto: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><mailto: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><mailto: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
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Received on Tue Dec 18 2018 - 10:00:04 PST
