From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 29 2011 - 04:33:39 CDT
This is very unlikely a Fedora problem and more likely a problem with your shell's path. Check your path environment variable to insure /usr/bin is listed in your path. If so, check that the namd/charmrun binaries or links to namd and charmrun exit in /usr/bin.
To check your path:
In bash: echo $PATH
In csh or tcsh: echo $PATH ; echo $path
To create a link, it's best you consult the manual: man ln. But you can create a link via: ln -s /path/to/namddir/namd2 /usr/bin/namd2
Best,
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 flavio seixas <oivalf_nix_at_yahoo.com> writes: > Date: Mon, 28 Mar 2011 06:55:57 -0700 (PDT) > From: flavio seixas <oivalf_nix_at_yahoo.com> > To: " ARL/WMRD)Michael S. Sellers (Cont" > <michael.s.sellers.ctr_at_us.army.mil> > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: namd and Fedora14 > Return-Path: <char_at_halifax.ks.uiuc.edu> > Message-ID: <741258.23117.qm_at_web162020.mail.bf1.yahoo.com> > X-Spam-Status: No, score=-2.5 required=5.0 tests=AWL,BAYES_00 > autolearn=unavailable version=3.1.7-0+tcb1 > > Hi Michael, > > Thank you for your help. > I am writing to let the list know that doing as your advice, namd works fine. > However, I needed to put the namd and charmrun pre compliled files at the same folder were input files were placed: > > ./charmrun ++local ./namd2 +p2 input.conf > output.log > > setting .bashrc our putting the compiled files on /usr/bin folder does not work. > > Thank you again. > > Flavio > > > > --- On Tue, 3/22/11, Michael S. Sellers (Cont, ARL/WMRD) <michael.s.sellers.ctr_at_us.army.mil> wrote: > > > From: Michael S. Sellers (Cont, ARL/WMRD) <michael.s.sellers.ctr_at_us.army.mil> > > Subject: Re: namd-l: namd and Fedora14 > > To: "flavio seixas" <oivalf_nix_at_yahoo.com> > > Cc: namd-l_at_ks.uiuc.edu > > Date: Tuesday, March 22, 2011, 3:10 PM > > 1. If this is a pre-compiled > > version of NAMD (ie Linux-x86_64), I believe they use > > "net-linux-..." compiled versions of Charm++. So, if > > you are running locally, you'll want to execute "charmrum > > ++local namd2 +p2 input.conf" > > > > 2. Generally it is not a good idea to run things like > > this as root. > > > > > > flavio seixas wrote: > > > Hi, > > > I was trying to run a namd simulation in an AMD Athlon > > X2 Fedora 14 Linux, when I found the following error > > message: > > > > > > [root_at_NIR set1]# charmrun namd2 +p2 input.conf > > > output.log > > > Charmrun> Couldn't find rsh program 'rsh'! > > > Charmrun> Couldn't find rsh program 'rsh'! > > > Charmrun> Error 1 returned from rsh (localhost:0) > > > > > > I do not find anything regarding this error on > > google. > > > > > > Someone have already found an error like this? > > > Regards, > > > > > > > > > Flavio > > > > > > > > > > > > > > > > > > > > > >
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