VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sat Dec 17 2016 - 13:14:38 CST

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>
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> 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.
>>
>> If you're having other issues aside from the rlwrap warnings, please
>> let us know, and be specific about what they are and/or what error
>> messages you are getting, if any, from VMD or from Linux.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Fri, Dec 16, 2016 at 10:49:21AM +0100, Francesco Pietra wrote:
>> > I must add that there is no vmd-1.9.3 problem with the workstation
>> (same
>> > OS as the problematic desktop, i.e., Debian GNU amd64 jessie stable,
>> > however graph interface Xfce; the gnome3 graph interface of the
>> > problematic desktop is, to my experience, another issue of gnome
>> since the
>> > introduction of version 3)
>> >
>> > francesco pietra
>> >
>> > ---------- Forwarded message ----------
>> > From: Francesco Pietra <[1]chiendarret_at_gmail.com>
>> > Date: Fri, Dec 16, 2016 at 8:43 AM
>> > Subject: vmd-l: vmd1.9.23 rlwrap: No match
>> > To: VMD Mailing List <[2]vmd-l_at_ks.uiuc.edu>
>> >
>> > Hallo:
>> >
>> > To replace vmd 1.9.2 I have now installed vmd 1 9.3 (
>> > vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz) on
>> Debian
>> > GNU Linux amd64 (Debian 8 jessy stable) using default /usr/local/bin
>> and
>> > /usr/local/lib (previous renaming the 1.9.2. version exec and lib)
>> > getting. At command "vmd", the error
>> >
>> > rlwrap: No match
>> >
>> > This is well known since many years but on Internet, as far as
>> packaging
>> > .deb is concerned, now I only find notes for ubunto, which, other
>> than
>> > being no GNU Linux, has nothing to do with Debian, except using the
>> same
>> > packaging mode.
>> >
>> > I was using a box without CUDA but I also have a workstation with
>> same OS,
>> > CUDA and GTX, where vmd 1.9.2 is working correctly.
>> > Thanks for advice
>> >
>> > francesco pietra
>> >
>> > References
>> >
>> > Visible links
>> > 1. mailto:chiendarret_at_gmail.com
>> > 2. mailto:vmd-l_at_ks.uiuc.edu
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>