VMD-L Mailing List
From: Cheri M Turman (Cheri.M.Turman_at_uth.tmc.edu)
Date: Tue Oct 26 2004 - 15:12:07 CDT
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Thanks so much, John. That solved it!
Cheers
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 1:43 pm
Subject: Re: vmd-l: error while loading shared libraries: libGLU.so.1
>
> 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
>
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