Re: Query for coarse grain system

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 05 2018 - 10:27:16 CDT

CUDA capability was significantly improved in 2.12, and refined in the
later versions (nightly). Try upgrading and see if it solves your
problem. For sure, the speedup would be worth the upgrade by itself.

Giacomo

On Thu, Apr 5, 2018 at 11:23 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
wrote:

> Dear Giacomo,
>
>
> Thanks for the reply.
>
> I am using namd 2.11 version. i have looked at the trajectories and they
> seems normal to me, for the CUDA-GPU the warning is coming still md is
> running similar to md on PC.
>
>
> Thanks
>
> Abhi
>
> Abhishek Tyagi,PhD
>
> Chemical and Biological Engineering
>
> Hong Kong University of Science and Technology
>
> Clear Water Bay, Hong Kong
>
>
> ------------------------------
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Thursday, April 5, 2018 11:17:47 PM
> *To:* NAMD list; Abhishek TYAGI
> *Subject:* Re: namd-l: Query for coarse grain system
>
> This is squarely a NAMD question: removing vmd-l.
>
> The CUDA compute kernels were significantly modified multiple times in the
> past versions. Without stating which versions you used, you are not really
> asking a question that can be answered.
>
> Also, have you looked at the trajectory before the error shows up? Well,
> this * will* involve VMD but there should be no question involved, since
> it should be standard practice to monitor the progress of the simulation.
>
> Giacomo
>
> On Thu, Apr 5, 2018 at 10:53 AM, Abhishek TYAGI <atyagiaa_at_connect.ust.hk>
> wrote:
>
> Hi,
>
>
> i am working on graphene-lipid system for coarse grain MD and I have
> encountered a strange problem (might be i don't understand it correctly). i
> need your suggestions to understand what is causing warning.
>
> During MD, when I run a system on CUDA based GPU (+p32; 4 GPU) system I
> encounter following error:
>
> Warning: Low global CUDA exclusion count! (6547 vs 6552) System unstable
> or pairlistdist or cutoff too small.
>
> i understand it is due to the reasons explained here
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.201
> 3-2014/3253.html, http://www.ks.uiuc.edu/Researc
> h/namd/mailing_list/namd-l.2009-2010/2786.html
> and here http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.201
> 0-2011/3814.html
>
> Although, when I run this same system on my linux PC I don't observe this
> error (+p8 1 GPU) and MD runs smoothly without any error or warning.
>
> Can any one please explain what I am missing here or what is potential
> problem I need to fix.
>
>
> Thanks in advance
>
> Abhi
>
>
> Abhishek Tyagi, PhD
>
> Chemical and Biological Engineering
>
> Hong Kong University of Science and Technology
>
> Clear Water Bay, Hong Kong
>
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:19:42 CST