Re: [AMBER] Error message from FEW in Amber14 tutorial A24

From: Jason Swails <>
Date: Sun, 22 Mar 2015 16:22:37 -0400

On Sun, Mar 22, 2015 at 2:19 PM, Michele Bonus <> wrote:

> Dear Michael,
> most probably this issue has its cause in Ubuntu's use of dash (Debian
> Almquist Shell) rather than bash or csh as the default shell.
> You could try to check the symlink of ~bin/sh, by either
> ls -l /bin/sh
> which might return "/bin/sh -> dash*"
> or
> file /bin/sh
> which might return "/bin/sh: symbolic link to `dash'".
> If the symlink is set to dash for your system, you could alter this to
> bash by
> ln -sf /bin/bash /bin/sh

​I would suggest against this. Ubuntu and Debian have good reasons for
using dash as the default shell, specifically the fact that it is much
lighter-weight and reduces the footprint of many components of the init
system, like openrc or systemd (and has other advantages; for instance,
"shellshock" did not affect Ubuntu systems, since the exploited
vulnerability was the on-POSIX part of bash [1]).

​he appropriate fix is in the script that is not POSIX sh-compliant.
Either fix the script to comply with the standard, or change the shebang
line to call bash explicitly. None of our programs should require users to
do something that substantially alters their core OS.

I couldn't tell from looking at the FEW directory where this script is --
do you know which script this is?



Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sun Mar 22 2015 - 13:30:02 PDT
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