From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 19 2016 - 16:07:55 CST

most of these rlwrap issues seem to be due to inconsistencies in
(t)csh implementations and requirements for or not escaping "special"
characters.
as john indicated, you can just comment out the whole stuff, or simply
remove the $VMDDIR/vmd_completion.dat file, as the problem is
triggered by the need to changing the list of "word delimiters" for
completion within the console.

however, the easiest solution here is to switch to the bourne shell
based startup script. the easiest way to achieve this would be to
temporarily tcsh, (re-)install vmd, and then re-install tcsh.

since (t)csh is becoming increasingly obsolete and fewer people are
familiar with it, there is little benefit to using it as a default.
i would suggest to even change the preference of the csh version over
the sh version of the vmd startup script in the installation.

i've been happily running (t)csh-free linux desktops, laptops and
workstations for many years now and never ran into any trouble with
vmd.

axel.

On Sat, Dec 17, 2016 at 8:06 PM, Strahs, Dr. Daniel Bernard
<dstrahs_at_pace.edu> wrote:
>
> I'm using Ubuntu 16.04 32-bit (old laptop, I know). rlwrap was causing problems, so I'm using vmd after uninstalling rlwrap. VMD 1.9.2 was built from source.
>
> With rlwrap installed:
>
> strahs_at_Hawker$ /usr/local/bin/vmd
> rlwrap: No match.
>
> With rlwrap uninstalled:
>
> strahs_at_Hawker$ /usr/local/bin/vmd
> rlwrap: Command not found.
> Info) VMD for LINUX, version 1.9.2 (December 2, 2016)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 2 CPUs detected.
> Info) Free system memory: 1207MB (60%)
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: Mesa DRI Intel(R) 945GM x86/MMX/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (2048x2048), 3-D (256x256x256), Multitexture (8)
> vmd > quit
> Info) VMD for LINUX, version 1.9.2 (December 2, 2016)
> Info) Exiting normally.
>
> As you can see, VMD-without-rlwrap reports "rlwrap not found", but then operates normally. In contrast, VMD-with-rlwrap is producing the "No match" error; this is produced from the rlwrap call in the vmd start script.
>
> I've been using VMD 1.9.2 without rlwrap for a couple of months now.
>
> Dan Strahs
> Biology Dept
> Pace University
>
>
>
> ________________________________
> From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Chitrak Gupta <chgupta_at_mix.wvu.edu>
> Sent: Saturday, December 17, 2016 2:14 PM
> To: Francesco Pietra
> Cc: John Stone; VMD Mailing List
> Subject: Re: Fwd: vmd-l: vmd1.9.23 rlwrap: No match
>
> I just wanted to chip in because I am having the exact same problem. I am using VMD 1.9.3 as well. Since I had to use VMD urgently I uninstalled rlwrap, so I can currently launch VMD, but with the "rlwrap: command not found" error.
>
>
> Chitrak.
>
> On Sat, Dec 17, 2016 at 3:42 AM, Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>> wrote:
> Hi John:
> Thanks for your answer. Sorry that you found my messages confusing. I wanted to say that I have two linux boxes at the same router, both running Debian GNU Linux amd 64 v8 jessie (stable). The box with two GPUs/CUDA, Xfce graphical interface, installed vmd-1.9.3 without any modification to scripts, i.e., no rlwrap problem. The simpler box, without GPUs, gnome3 graphical interface, reported rlwrap issues, as follows
>
> francesco_at_tya64:~$ which vmd
> /usr/local/bin/vmd
> francesco_at_tya64:~$ vmd
> rlwrap: No match.
> francesco_at_tya64:~$
>
>
> I have now applied your suggestions (hopefully correctly), i.e., in uncompressed/untarred /vmd-1.9.3/bin/vmd.sh (as requested superuser)
>
> # detect if we have rlwrap available to have commandline editing
> ## case $MACHARCH in
> ## *Linux*)
> ## if hash rlwrap 2>/dev/null
> ## then
> ## if [ -f "${MASTERVMDDIR}/vmd_completion.dat" ]
> ## then
> ## vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f ${MASTERVMDDIR}/vmd_completion.dat "
> ## else
> ## vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
> ## fi
> ## else
> ## vmdprefixcmd=""
> ## fi
> ## ;;
> ##
> ## *)
> ## vmdprefixcmd=""
> ## ;;
> ## esac
> vmdprefixcmd=""
>
>
>
> Then, as user, I run ./configure. Then, from /src, as superuser, I run <make install>, getting the vmd executable in /usr/local/bin and vmd directory in /usr/local/lib. Same rlwrap issues as before (even after rebooting)
>
> francesco_at_tya64:~$ which vmd
> /usr/local/bin/vmd
> francesco_at_tya64:~$ vmd
> rlwrap: No match.
> francesco_at_tya64:~$
>
> I assume not to have followed your indications correctly and therefore I apologized for wasting your time.
>
> Sincerely
>
> francesco pietra
>
> On Fri, Dec 16, 2016 at 9:14 PM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
> Francesco,
> From your emails, I'm having a hard time determining what problem(s)
> you are or are not having.
> I gather from the previous email that you get the warning about 'rlwrap',
> but your emails were unclear about whether you were having any other problem?
>
> You can prevent the rlwrap problem by commenting out the associated code in the VMD startup script by commenting out the following lines of text in the
> so they look as below:
>
> csh variant of VMD startup script:
> ----------------------------------
> # detect if we have rlwrap available to have commandline editing
> set vmdprefixcmd=""
> ## if (("${ARCH}" == "LINUX") || ("${ARCH}" == "LINUXAMD64")) then
> ## set rlwrap=`which rlwrap`
> ## if ( -x "$rlwrap" ) then
> ## if ( -f ${MASTERVMDDIR}/vmd_completion.dat ) then
> ## set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f ${MASTERVMDDIR}/vmd_completion.dat "
> ## else
> ## set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
> ## endif
> ## endif
> ## endif
>
>
> sh/bash variant of VMD startup script:
> --------------------------------------
> # detect if we have rlwrap available to have commandline editing
> ## case $MACHARCH in
> ## *Linux*)
> ## if hash rlwrap 2>/dev/null
> ## then
> ## if [ -f "${MASTERVMDDIR}/vmd_completion.dat" ]
> ## then
> ## vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f ${MASTERVMDDIR}/vmd_completion.dat "
> ## else
> ## vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
> ## fi
> ## else
> ## vmdprefixcmd=""
> ## fi
> ## ;;
> ##
> ## *)
> ## vmdprefixcmd=""
> ## ;;
> ## esac
> vmdprefixcmd=""
>
>
> If you do this, it will disable the use of 'rlwrap' in the VMD startup code
>
>

-- 
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.