VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Dec 17 2016 - 02:42:26 CST

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/
>