VMD-L Mailing List

From: Cheri M Turman (Cheri.M.Turman_at_uth.tmc.edu)
Date: Tue Oct 26 2004 - 13:37:56 CDT

John,
There is a problem here using the command you supplied. Here is what I got:

[cheri_at_dhcp-169-77 cheri]$ cd PROGRAMS/VMD/RUNVMD
[cheri_at_dhcp-169-77 RUNVMD]$ vmd -dispdev text
/home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/vmd_LINUXAMD64: Command not found.

This made me think I should have configured with LINUXAMD64 instead of
LINUX. I tried that but the installation did not work properly. I see
that make install could not find vmd_LINUXAMD64 executable. When I go
to the vmd_scripts/vmd dir, this executable isn't there. So, I went
back to the working vmd dir where I unzipped VMD originally
(home/cheri/PROGRAMS/VMD/vmd-1.8.2), and saw that the dir LINUXAMD64
had nothing in it. Any thoughts? Here is the console as I went through
the install of LINUXAMD64:
 
[cheri_at_dhcp-169-77 cheri]$ cd PROGRAMS/VMD/vmd-1.8.2/
[cheri_at_dhcp-169-77 vmd-1.8.2]$ ./configure
using configure.options: LINUX OPENGL TK IMD TCL PYTHON
[cheri_at_dhcp-169-77 vmd-1.8.2]$ ./configure LINUXAMD6 OPENGL TK IMD TCL
PYTHON
Architecture LINUXAMD6 not supported (IRIX6 IRIX6_64 FREEBSD HPUX11 AIX4
LINUX L INUXALPHA LINUXAMD64 LINUXPPC MACOSX TRU64 SOLARIS2 SOLARIS2_64
SOLARISX86 WIN32 )
[cheri_at_dhcp-169-77 vmd-1.8.2]$ ./configure LINUXAMD64 OPENGL TK IMD TCL
PYTHON
[cheri_at_dhcp-169-77 vmd-1.8.2]$ cd src/
[cheri_at_dhcp-169-77 src]$ make install
if [ ! -d /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd ]; then \
        mkdir -p /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd ; \
fi ; \
if [ ! -d /home/cheri/PROGRAMS/VMD/RUNVMD ]; then \
        mkdir -p /home/cheri/PROGRAMS/VMD/RUNVMD ; \
fi ; \
if [ ! -d /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/doc ]; then \
        mkdir -p /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/doc; \
fi
cp ../Announcement /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cp ../README /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cp ../LICENSE /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cp ../doc/ug.pdf /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/doc
cp ../LINUXAMD64/vmd_LINUXAMD64 /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory
make: [install] Error 1 (ignored)
cp ../lib/stride/stride_LINUXAMD64 ../lib/surf/surf_LINUXAMD64
../lib/tachyon/ta chyon_LINUXAMD64 /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cp: cannot stat `../lib/stride/stride_LINUXAMD64': No such file or directory
cp: cannot stat `../lib/surf/surf_LINUXAMD64': No such file or directory
cp: cannot stat `../lib/tachyon/tachyon_LINUXAMD64': No such file or
directory
make: [install] Error 1 (ignored)
cd ..; tar -cf - scripts | \
(cd /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd ; tar -xf -)
cd ../lib; tar -cf - scripts | \
(cd /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd ; tar -xf -)
cd ..; tar -cf - python | \
(cd /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/scripts ; tar -xf -)
cd ..; tar -cf - plugins | \
(cd /home/cheri/PROGRAMS/VMD/vmd_scripts/vmd ; tar -xf -)
cp ../data/.vmdrc ../data/.vmdsensors
/home/cheri/PROGRAMS/VMD/vmd_scripts/vmd
cd ../bin ; \
if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
echo '#!/bin/csh' >> run_vmd_tmp ; \
echo 'set defaultvmddir=/home/cheri/PROGRAMS/VMD/vmd_scripts/vmd' >>
run_vmd_tmp ; \
echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
cat vmd >> run_vmd_tmp ; \
chmod +x run_vmd_tmp ; \
cp run_vmd_tmp /home/cheri/PROGRAMS/VMD/RUNVMD/vmd ; \
rm -f run_vmd_tmp
echo Make sure /home/cheri/PROGRAMS/VMD/RUNVMD/vmd is in your path.
Make sure /home/cheri/PROGRAMS/VMD/RUNVMD/vmd is in your path.
echo "VMD installation complete. Enjoy!"
VMD installation complete. Enjoy!
[cheri_at_dhcp-169-77 src]$ cd ../../RUNVMD
[cheri_at_dhcp-169-77 RUNVMD]$ ./vmd
[1] 13139
[cheri_at_dhcp-169-77 RUNVMD]$ vmd -dispdev text
/home/cheri/PROGRAMS/VMD/vmd_scripts/vmd/vmd_LINUXAMD64: Command not found.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030 USA

    e-mail: cheri.m.turman_at_uth.tmc.edu
    Ph.: 713-500-6126
    Fax: 713-500-0652

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Tuesday, October 26, 2004 12:38 pm
Subject: Re: vmd-l: error while loading shared libraries: libGLU.so.1

>
> Cheri,
> Run this command and tell me what you get:
> vmd -dispdev text
>
> If that works, then the next thing to try would be:
> source /usr/local/bin/vmd (wills start/exit as before)
> then:
> /usr/local/lib/vmd/vmd_LINUX
>
> Tell me what you get from those steps and I should be able to
> determine what's wrong.
>
> We have VMD working fine on a 64-bit WS3 machine here, so I'm
> certain I can help you get yours working as well.
>
> John
>
>
> On Tue, Oct 26, 2004 at 12:21:29PM -0500, Cheri M Turman wrote:
> > Hi John,
> > I think the rpm you suggested works fine now but I have a new
> problem.
> > When I execute vmd, it appears as if the startup window is
> opening but
> > it just flashes and then disappears. Do you think this leads
> back to
> > the libs again or is this something else? If you have no
> suggestions, I
> > may try wiping RH WS3 and going back to debian or xandros since
> these> are the OS I am use to running VMD and NAMD on. This is the
> first time
> > of many that I have had so much trouble installing VMD. It is
> normally> simple and since I am having issues installing other
> programs on RH WS3,
> > I am thinking RH WS3 is not worth the trouble!
> > Cheers,
> > Cheri
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Cheri M. Turman
> > Graduate Student
> > University of Texas-Houston Medical School
> > 6431 Fannin
> > Houston, TX 77030 USA
> >
> > e-mail: cheri.m.turman_at_uth.tmc.edu
> > Ph.: 713-500-6126
> > Fax: 713-500-0652
> >
> > ----- Original Message -----
> > From: John Stone <johns_at_ks.uiuc.edu>
> > Date: Thursday, October 21, 2004 3:20 pm
> > Subject: Re: vmd-l: error while loading shared libraries:
> libGLU.so.1>
> > >
> > > Cheri,
> > > I did some more digging on this, and as it turns out, the RH
> WS3
> > > installation doesn't seem to install the 32-bit GLU RPM by
> default, or
> > > at least not consistently. We fixed our machine here by doing
> this:> > rpm -force -UVh XFree86-Mesa-libGLU-4.3.0-68-EL.i386.rpm
> > >
> > > I think that if you're only problem is the missing GLU library,
> you> > will be able to fix your machine by following that step
> (with the
> > > appropriateRPM file sitting in the working directory when you
> run
> > > the command...)
> > >
> > > We're not sure why RH didn't install the 32-bit GLU library in the
> > > installation by default, but that seems to cure the type of
> problem> > you're having.
> > >
> > > John
> > >
> > > On Thu, Oct 21, 2004 at 01:24:12PM -0500, Cheri M Turman wrote:
> > > > Hi all,
> > > > I just got a new dual xeon system and I'm trying to load vmd.
> It
> > > seems> I am having the same issue with most programs I'm trying
> to
> > > install on
> > > > this system. I am running redhat enterprise WS3 and there
> are
> > > always> problems loading shared libraries. It seems that RH
> dist have
> > > > completely changed common dir between the typical RH7-9
> versus RH WS
> > > > versions.
> > > >
> > > > Anyway, with vmd, the problem is with libGLU.so.1. This lib
> is in
> > > > /usr/X11R6/lib64/. I made a symbolic link to /usr/X11R6/lib/
> but
> > > this> doesn't seem to be the right dir either. Can anyone
> direct
> > > me where
> > > > this lib should be/where vmd wants it to be?
> > > > Thanks,
> > > > Cheri
> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > > Cheri M. Turman
> > > > Graduate Student
> > > > University of Texas-Houston Medical School
> > > > 6431 Fannin
> > > > Houston, TX 77030 USA
> > > >
> > > > e-mail: cheri.m.turman_at_uth.tmc.edu
> > > > Ph.: 713-500-6126
> > > > Fax: 713-500-0652
> > >
> > > Content-Description: Card for Cheri M Turman
> > > <Cheri.M.Turman_at_uth.tmc.edu>
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>
> > >
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
>
> Content-Description: Card for Cheri M Turman
> <Cheri.M.Turman_at_uth.tmc.edu>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>