VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 31 2020 - 14:25:47 CST

Hi,
  I missed this discussion due to being a crunch period when it
got posted. The issue here is that the existing versions of QwikMD
don't know how to launch NAMD versions other than the straight CPU
versions. So, in general, if you want to use QwikMD with NAMD
for an interactive run, you'll need the plain old CPU version of
NAMD for that purpose. You can of course run the GPU-accelerated
builds of NAMD yourself, but that's beyond QwikMD's knowledge at
the present time, since there are so many extra flags and details
in those cases.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 07, 2020 at 03:49:51PM -0800, John Keller wrote:
> Further info: QwikMD runs fine with the multi-core, non-CUDA NAMD
> installed. (NAMD_Git-2020-09-21_Linux-x86_64-multicore). So the problem is
> related to the GPU, or the CUDA version. BTW, using 24 threads, the 1ubq
> simulation runs at about 90 ns/day.
> John K.
> On Wed, Oct 7, 2020 at 1:31 PM John Keller <[1]jwkeller_at_alaska.edu> wrote:
>
> Hi All,
> Running the QwikMD tutorial starting with 1ubq.pdb, several repeated
> simulations have lasted 2 -20 psec before exiting with an error. "IMD
> connection ended unexpectedly."Â "2" processors were chosen after
> hitting Start MD Simulation.
> This is a workstation with CentOS 8.2, 24-core Threadripper with SMT,
> 128 GB memory, GTX 980 with nvidia driver 155.23.05 and CUDA v 11.1.
> Same result whether or not ASLR is turned on.
> VMD 1.9.3 CUDA8-OptiX4-OSRay111p1, NAMD Git-2020-09-21
> Â Linux-x86_64-multicore-CUDA, and qwikmd_beta are installed.
> Do I have the correct versions of VMD/NAMD/QwikMD?
> John Keller
> Department of Chemistry & Biochemistry
> University of Alaska Fairbanks
>
> References
>
> Visible links
> 1. mailto:jwkeller_at_alaska.edu 

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