From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 29 2011 - 04:36:36 CDT
Just now saw Michael's more detailed instructions. Please defer to them over my shorter message.
-- 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 "Michael S. Sellers (Cont, ARL/WMRD)" <michael.s.sellers.ctr_at_us.army.mil> writes: > Date: Mon, 28 Mar 2011 10:12:47 -0400 > From: "Michael S. Sellers (Cont, ARL/WMRD)" > <michael.s.sellers.ctr_at_us.army.mil> > To: flavio seixas <oivalf_nix_at_yahoo.com> > CC: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: namd and Fedora14 > Return-Path: <char_at_halifax.ks.uiuc.edu> > Message-ID: <4D90975F.9010609_at_us.army.mil> > X-Spam-Status: No, score=-2.6 required=5.0 tests=AWL,BAYES_00 > autolearn=unavailable version=3.1.7-0+tcb1 > > Glad that worked for you. > > There are ways to setup links or your path variable so you can refer > to namd2 and charmrun without a full path or copying everything into > a folder... > > You could try, as root: ln -s /path/to/NAMD/namd2 /usr/bin/namd2; > ln -s /path/to/NAMD/charmrun /usr/bin/charmrun, if /usr/bin is in > your path. ***I believe with Fedora, /usr/bin is not in the path > variable by default. This might have changed in newer releases, or > I may be wrong. echo $PATH. > > If you added your NAMD folder to your path variable via .bashrc, as > export PATH=$PATH:/path/to/NAMD/, then it should also work. > Remember to start a new bash session after editing it. > > -Mike > > flavio seixas wrote: > >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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