VMD-L Mailing List

From: Strahs, Dr. Daniel Bernard (dstrahs_at_pace.edu)
Date: Sat Dec 17 2016 - 15:23:08 CST

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--_000_14820097884196814paceedu_--