RE: NAMD+PLUMED

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sat Jun 02 2018 - 22:03:22 CDT

Just my two cents: PLUMED and Colvars both effectively ignore the GPU, and only do the calculations on the CPU. The rest of the MD dynamics will use GPUs as appropriate, but if your collective variable isn't reasonable, it may well end up bottlenecking performance with both codes.

-Josh

On 2018-06-02 15:31:08-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hi, the use of GPUs is supported with either code, in that the GPU-enabled version of NAMD can run with either Colvars, or PLUMED if you specifically compile it with NAMD.
The error you saw was probably unrelated to the combination of Colvars, metadynamics and GPU.
As for the performance, you need to give some specifics regarding, the type of system and the type of collective variables, and the hardware you plan on running on, to get useful advice.
Regards,
Giacomo

On Sat, Jun 2, 2018 at 2:34 PM, jing liang <jingliang2015_at_gmail.com<mailto:jingliang2015_at_gmail.com>> wrote:
Hi,
I tried to run a Metadynamics simulation in NAMD using Colvars on a GPU
card but it seems that this type of simulations is not supported yet on GPUs,
right?
Then, I read about an alternative for Colvars called PLUMED. Do you know
if NAMD+PLUMED can be run on GPUs?
Compared to Colvars, does PLUMED runs faster or scales better with the
number of cores for instance?
Any comment is welcome.

--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQUQjRXJmJsjQs9BNrMBuDkjMB9g8UoXg%3D&reserved=0>
https://github.com/giacomofiorin1&sdata=axs0l%2FR20jfyHHX3nAVPzvw4xEVebcdyAPfqt9R5kUw%3D&reserved=0>

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:19:56 CST