Re: [AMBER] New to AMBER, installation issues

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 12 Oct 2011 16:50:22 -0400

On Wed, Oct 12, 2011 at 4:11 PM, peker milas <pekermilas.gmail.com> wrote:

> Hi Matt,
>
> Ubuntu's primary shell environment is "dash" not "bash".


This is only partially true, really. It's true that /bin/sh points to dash
instead of bash, so any script that specifically invokes /bin/sh on the
shebang line (#!/bin/sh) will have that script interpreted using the dash
shell. However, unless you specifically change the following option (which
is very unlikely for the OP), Ubuntu creates new users that have their
default shell pointing to bash, not sh or dash. You can prove this to
yourself by opening up a terminal (or going to TTY1 through TTY6 and logging
in) and typing the command

echo $SHELL

which should return /bin/bash. Also, dash supports most features of bash
(only missing some features that are not POSIX standard, anyway). This is
not the cause of his problems, in any case.

Therefore as a
> starting point you may want to redirect your shell environment to real
> "bash". If you like you may use a command as following;
>

> sudo rm /bin/sh; sudo ln /bin/bash /bin/sh
>

This is the approach I used to take (when I was sick of seeing "Bad fd
number" trying to run scripts that claimed /bin/sh-compatibility but were
really designed for bash), but I now suggest against it. The choice to use
dash by the Ubuntu team wasn't a haphazard accident -- they chose it because
it is a lighter-weight shell with reduced overhead for starting up. As
such, I suggest that people leave those links alone (though of course people
are free to do what they want). However, I've messed around in main system
directories too much thinking I knew what I was doing only to have it bite
me in the end (like moving malloc.h from /usr/include/malloc/ to
/usr/include on my Mac OS X systems, only to have that break MacPorts GCC
builds in some obscure way later on down the line).

All the best,
Jason

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 12 2011 - 14:00:05 PDT
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