Tutorial-l Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Oct 08 2018 - 09:22:31 CDT

Hi Noah,

would it be possible to post the output messages that you are getting when
you start the simulation?

In practice, the NAMD version that you should be using is one of these"

   - Linux-x86_64-netlrts
   <https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1529>
(Multi-copy
   algorithms)
   - Linux-x86_64-netlrts-smp-CUDA
   <https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1538>
(Multi-copy
   algorithms, single process per copy)

Best

João

On Sat, Oct 6, 2018 at 3:32 PM Schwartz, Noah <nws9g2_at_mail.missouri.edu>
wrote:

> Hi,
>
> I am trying to follow the "1-D REUS" tutorial on my laptop. I am using a
> Dell G3 with an i5-8300H and NVIDIA Geforce 1050, and Ubuntu 18.04 LTS. I
> am a relative beginner to Linux (installed about a month ago) and have been
> using NAMD for about 4 months. I am just an undergrad, but I have tried to
> thoroughly search google, the mailing list, and the release notes before
> posting here.
>
> I believe my problem is concerning which version of NAMD to use, but I
> could be wrong about that. After reading the release notes, I realize that
> I need to use a version with multi-copy algorithms enabled. I have gone
> down the list on the download page and tried using the 'ibverbs','netlrts',
> and 'verbs' with and without smp and cuda but without avail. I have also
> tried compiling my own build of NAMD but that created a new headache
> (followed the instructions on the release notes but got a recipe error on
> the final step; I can post in more detail if compiling is truly the way to
> go).
>
> I am trying to run the line 'charmrun namd2 ++local +p8 +replicas 8
> job0.conf +stdout output/out.%d.log'. I have specified the path to
> umbrella.namd as the tutorial says, and placed whichever builds of charmrun
> and namd I was testing in my path. I have also tried additional options
> such as ++ppn 8 or ++mpiexec just to see what happens, but I don't
> understand their purpose.
>
> Whichever version I use I get the message 'Scalable Start Enabled' and
> then immediately after the message 'Killed'. I don't believe it is even
> reading the configuration file since no output is being generated.
>
> My goal is to complete this tutorial so that I can implement replica
> exchange umbrella sampling on my PI's (significantly more powerful)
> workstation and use it for my project. If anyone could tell me where I am
> going wrong, or can refer me to a resource that I may have missed, I would
> greatly appreciate it. I can also add any additional information that would
> be helpful to solve this problem.
>
> Thanks,
>
> Noah Schwartz
>
> 

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851
**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**