Re: Consulting about buying new hardware (GPU)

From: Lewis J Martin (
Date: Wed Jul 11 2018 - 18:13:10 CDT

In my experience GPUs are powerful enough that most workstations will be
limited by the number of CPUs. If you plan on using NAMD 2.13 when it is
released then this might change.

Pragmatically it might be better to consider price/performance ratio.
P100 comes with a lot of features that are good for HPC centres, such as
ECC, but are less useful in a workstation for molecular dynamics. A
1080Ti or Titan XP are a fraction of the cost, and you can use the extra
money to buy more CPUs or GPUs right now or down the track.

 From memory I was limited by CPU using a single Titan XP, 20 CPUs
(Intel Xeon Gold 6138) on a system of ~150,000 atoms with NAMD 2.12.



On 11/7/18 4:07 pm, namd-l digest wrote:
> Date: Tue, 10 Jul 2018 22:45:27 +0800
> From: JC Gumbart<>
> Subject: Re: namd-l: Consulting about buying new hardware (GPU)
> I just did a test with a 382k-atom system on a p100 and a v100, each with 8 cpus. I get the same performance for NAMD on both (~5.3 ns/day), indicating that itbs CPU-starved. With the p100, the GPU utilization is 33%, while with the v100, its 20%. I doubt that 16 cores would change this comparison enough to differentiate the two.
> Best,
> JC
>> On Jul 10, 2018, at 4:44 PM, michael zhenin<> wrote:
>> Hi all,
>> We are interested in buying new GPU card for simulating relatively big systems (more than 300K atoms) using NAMD 2.12 version.
>> Currently we have one P100 card (with 16 "real" cpu cores) that is quite fast - around 10 ns/day for that system size.
>> We were wondering if there is any recommendation/experience with other cards that will speed up the simulation time. Specifically, V100 PCIE, TITAN-V ,or GTX-1080TI.
>> Many thanks,
>> Michael.

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