VMD-L Mailing List

From: Daniel Strahs (dstrahs_at_pace.edu)
Date: Fri Aug 01 2014 - 16:16:13 CDT

On Fri, 2014-08-01 at 16:51 -0400, Axel Kohlmeyer wrote:
> On Fri, Aug 1, 2014 at 4:34 PM, Daniel Strahs <dstrahs_at_pace.edu> wrote:
> > Following up on this message thread:
> >
> > Installing VMD 1.9.1 in Ubuntu 14.04.1 LTS on an i386 laptop:
> >
> > #1) Initial install from source ran VMD with initial error message:
> > "rlwrap: command not found". This was due to a non-installation of
> > rlwrap.
>
> hmm... the script should continue not terminate.

Please note that I said "ran VMD with initial error message". The script
did indeed continue, and did not terminate.

> > #2) Installed rlwrap. Now VMD refused to run; error message was "rlwrap:
> > No match." Checked vmd start script in /usr/local/bin/vmd; vmdprefixcmd
> > was set properly to read "rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f
> > ${MASTERVMDDIR}/vmd_completion.dat"
> >
> > #3) Edited rlwrap command to eliminate word-breaking characters ie
> > "rlwrap -C vmd -c -f ${MASTERVMDDIR}/vmd_completion.dat"; vmd starts
> > normally
> >
> > #4) Added in the word-breaking characters carefully testing each
> > addition. Final working command is "rlwrap -C vmd -c -b(){}],&^%#;|\\ -f
> > ${MASTERVMDDIR}/vmd_completion.dat"
> >
> > The problem with Ubuntu is two-fold. First, rlwrap is choking on the "["
> > character for some reason. Second, it only happens when csh is invoked.
> > The original rlwrap command (including [) works find in tcsh.
>
> > I haven't clarified whether this is an rlwrap bug or a csh bug in Ubuntu
> > 14.04. The immediate solutions at the moment appear to be either editing
> > the "[" character out of rlwrap word-breaking characters or switching to
> > a different shell in the script, such as tcsh.
>
> at this point it is difficult to tell apart which is a bug or a
> feature. there are subtle differences between csh and tcsh and some
> what argue that both are equally broken. i am not going down that
> rabbit hole, but very obviously the script has only seen limited
> testing on a "real" csh.
>
> i also would like to point out another option: use the /bin/sh
> compatible version of the launcher script. the bourne shell on ubuntu
> is very standard conforming and thus chances are that it has less of
> an issue...
>
> axel.

Except that some of the commands such as set and setenv would need to be
reformatted. Again, a rabbit hole, although as you note, probably of
limited depth... :)

A 3rd option is to just uninstall rlwrap, and live with the error
message and the lack of command-line editing. Quite liveable.

> >
> > --
> > Daniel B. Strahs
> > Associate Professor
> > Biology and Health Sciences Department
> > Pace University, New York
> >
> >
> > On Mon, 2014-03-03 at 09:32 -0500, Axel Kohlmeyer wrote:
> >> On Mon, Mar 3, 2014 at 9:24 AM, Subbarao Kanchi <ksubbu85_at_gmail.com> wrote:
> >> > Dear AXel,
> >> > It worked well before. It is ubuntu 12.04, I install lapack
> >> > library recently. After that I tried by uninstall the libraries but it is
> >> > giving same error.
> >>
> >>
> >> this has nothing to do with lapack. nothing at all. there has to be
> >> something else. some update/change to the shell program you are using.
> >> or you re-installed VMD and it picked a different shell this time. as
> >> i mentioned, try out the latest alpha test version of VMD and let us
> >> know if that still produces the same message.
> >>
> >> axel.
> >>
> >> >
> >> > Regards,
> >> >
> >> >
> >> >
> >> >
> >> > On Mon, Mar 3, 2014 at 7:45 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >> >>
> >> >> On Mon, Mar 3, 2014 at 8:34 AM, Subbarao Kanchi <ksubbu85_at_gmail.com>
> >> >> wrote:
> >> >> > Dear All,
> >> >> > VMD is giving an error "rlwrap: No match.", then I
> >> >> > followed
> >> >> > the suggestion given by Pablo De Biase in the mailing list and it works
> >> >> > fine after removing -b orguments
> >> >> > (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19158.html). I
> >> >> > am
> >> >> > not able to understand that "rlwrap -C vmd -c -b(){}[],&^%#;|\\" is not
> >> >> > working suddenly. I will appreciate any comments regarding this.
> >> >>
> >> >> why "suddenly"? did it work before? if yes, what did you change? have
> >> >> you tried the latest alpha test version?
> >> >>
> >> >> axel.
> >> >>
> >> >>
> >> >> >
> >> >> > Regards,
> >> >> > Subbarao Kanchi.
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >> College of Science & Technology, Temple University, Philadelphia PA, USA
> >> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> >
> >> >
> >>
> >>
> >>
> >
> >
> >
>
>
>