VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 26 2004 - 13:43:49 CDT

Cheri,
  Yeah, that's the result I expected, since you're running 1.8.2.
All you need to do to fix this is delete these two lines from
your /usr/local/bin/vmd startup script:
    else if (`uname --machine` == "x86_64") then
    set ARCH=LINUXAMD64

Once those two lines are deleted, you should be in business.
Don't bother trying to reinstall in a different way, as it's
an issue with that startup script that shipped with VMD 1.8.2.

The next version of VMD has a smarter startup script that will
fall-back to the 32-bit version if the 64-bit build isn't there.

  John

On Tue, Oct 26, 2004 at 01:37:56PM -0500, Cheri M Turman wrote:
> 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
> >

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