Tutorial-l Mailing List

From: Schwartz, Noah (nws9g2_at_mail.missouri.edu)
Date: Sat Oct 06 2018 - 15:31:41 CDT

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

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**