VMD-L Mailing List

From: Archana Sonawani-Jagtap (ask.archana_at_gmail.com)
Date: Fri Nov 25 2016 - 07:02:34 CST

Hi,

Thank you so much...I could install VMD.

On Thu, Nov 24, 2016 at 9:18 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Okay, you are very close now. This remaining error occurs because your
> system is missing libGLU, which is required by the older versions of VMD.
>
> The latest (beta4, and the soon final release) version of VMD 1.9.3 no
> longer
> requires libGLU, so if this is the only issue that remains, you could
> get past this by installing the VMD 1.9.3 beta4 version that's on the
> web site, or the final release of VMD 1.9.3 which should be posted in the
> next few days, since they no longer require libGLU. This is going to be
> the easiest approach I think. Since libGLU was missing, I also recommend
> that you run "glxinfo" and make sure you don't get any errors in case there
> are any other issues with the graphics software and drivers on your system.
>
> If you want to run VMD 1.9.2 or older versions (or any other program that
> needs to use libGLU), you will need to install the missing libGLU
> shared library on your system.
> You'll have to determine what package to install to get libGLU on your
> system. Most Linux systems historically included libGLU with the standard
> OpenGL package, but clearly yours doesn't have it. There are a number of
> suggestions for common cases on this topic on stackoverflow.com, be wary
> of conflicts between newly installed OpenGL packages and your graphics
> drivers which may require you to reinstall the graphics drivers too:
> http://stackoverflow.com/questions/22360771/missing-
> recommended-library-libglu-so
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Nov 24, 2016 at 02:26:44PM +0530, Archana Sonawani-Jagtap wrote:
> > Hi,
> >
> > Sorry for misunderstanding..I tried installing
> > vmd-1.9.2.bin.LINUXAMD64.opengl.tar.gz in my laptop, but I still get
> this
> > error when I type vmd:
> >
> > /usr/local/lib/vmd/vmd_LINUXAMD64: error while loading shared
> libraries:
> > libGLU.so.1: cannot open shared object file: No such file or directory
> >
> > On Thu, Nov 24, 2016 at 1:02 PM, John Stone <[1]johns_at_ks.uiuc.edu>
> wrote:
> >
> > Hi,
> > A I think you misunderstood about the approach to installing the
> > 64-bit version.A When you run the configure script, you should not
> be
> > passing any parameters, otherwise it will look for files that don't
> > exist
> > in the binary distribution (thus all of the errors below).A What I
> > meant
> > when I suggested that you install the LINUXAMD64 build of VMD, is
> that
> > you need to start over, and go download one of the LINUXAMD64 tar
> files
> > from the VMD web site and then install that using the standard
> install
> > procedure for unix/linux.
> >
> > Cheers,
> > A John Stone
> > A [2]vmd_at_ks.uiuc.edu
> >
> > On Thu, Nov 24, 2016 at 12:42:42PM +0530, Archana Sonawani-Jagtap
> wrote:
> > >A A Hi,
> > >
> > >A A I tried ./configure LINUXAMD64, but still I get the following
> > after make
> > >A A install:
> > >
> > >A A if [ ! -d "/usr/local/lib/vmd" ]; then \
> > >A A A A AA mkdir -p "/usr/local/lib/vmd" ; \
> > >A A fi ; \
> > >A A if [ ! -d "/usr/local/bin" ]; then \
> > >A A A A AA mkdir -p "/usr/local/bin" ; \
> > >A A fi ; \
> > >A A if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
> > >A A A A AA mkdir -p "/usr/local/lib/vmd"/doc; \
> > >A A fi
> > >A A cp ../AnnouncementAA "/usr/local/lib/vmd"
> > >A A cp ../READMEA A A A A A AA "/usr/local/lib/vmd"
> > >A A cp ../LICENSEA A A A A AA "/usr/local/lib/vmd"
> > >A A cp ../doc/ug.pdfA A A A A A AA "/usr/local/lib/vmd"/doc
> > >A A if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
> > >A A A A A A A A A A A AA mv -f "/usr/local/lib/vmd/vmd_
> LINUXAMD64"
> > >A A "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; rm -f
> > >A A "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
> > >A A cp ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
> > >A A cp: cannot stat a**../LINUXAMD64/vmd_LINUXAMD64a**: No such
> file
> > or
> > >A A directory
> > >A A make: [install] Error 1 (ignored)
> > >A A if [ -d "../lib/redistrib/lib_LINUXAMD64" ]; then \
> > >A A A A AA cd ../lib/redistrib/lib_LINUXAMD64; tar -cf - ./* |
> \
> > >A A A A AA (cd "/usr/local/lib/vmd" ; tar -xf -) \
> > >A A fi ;
> > >A A cp ../lib/stride/stride_LINUXAMD64
> ../lib/surf/surf_LINUXAMD64
> > >A A ../lib/tachyon/tachyon_LINUXAMD64 "/usr/local/lib/vmd"
> > >A A cp: cannot stat a**../lib/stride/stride_LINUXAMD64a**: No
> such
> > file or
> > >A A directory
> > >A A cp: cannot stat a**../lib/surf/surf_LINUXAMD64a**: No such
> file
> > or
> > >A A directory
> > >A A cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No
> such
> > file or
> > >A A directory
> > >A A make: [install] Error 1 (ignored)
> > >A A cd ..; tar -cf - scripts | \
> > >A A (cd "/usr/local/lib/vmd" ; tar -xf -)
> > >A A cd ../lib; tar -cf - scripts | \
> > >A A (cd "/usr/local/lib/vmd" ; tar -xf -)
> > >A A cd ..; tar -cf - python | \
> > >A A (cd "/usr/local/lib/vmd"/scripts ; tar -xf -)
> > >A A cd ..; tar -cf - plugins | \
> > >A A (cd "/usr/local/lib/vmd" ; tar -xf -)
> > >A A cd ..; tar -cf - shaders | \
> > >A A (cd "/usr/local/lib/vmd" ; tar -xf -)
> > >A A if [ -f ../LINUXAMD64/OptiXShaders.ptx ]; then \
> > >A A A A AA cp ../LINUXAMD64/OptiXShaders.ptx
> > "/usr/local/lib/vmd/shaders"; \
> > >A A fi;
> > >A A cp ../data/.vmdrc ../data/.vmdsensors
> ../data/vmd_completion.dat
> > >A A "/usr/local/lib/vmd"
> > >A A cd ../bin ; \
> > >A A if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
> > >A A if [ ! -x "/bin/csh" ]; then \
> > >A A A A AA echo "Info: /bin/csh shell not found, installing
> Bourne
> > shell
> > >A A startup script instead" ; \
> > >A A A A AA echo '#!/bin/sh' >> run_vmd_tmp ; \
> > >A A A A AA echo 'defaultvmddir="/usr/local/lib/vmd"' >>
> run_vmd_tmp
> > ; \
> > >A A A A AA echo 'vmdbasename=vmd' >> run_vmd_tmp ; \
> > >A A A A AA cat vmd.sh >> run_vmd_tmp ; \
> > >A A else \
> > >A A A A AA echo '#!/bin/csh' >> run_vmd_tmp ; \
> > >A A A A AA echo 'set defaultvmddir="/usr/local/lib/vmd"' >>
> > run_vmd_tmp ; \
> > >A A A A AA echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
> > >A A A A AA cat vmd.csh >> run_vmd_tmp ; \
> > >A A fi ; \
> > >A A chmod +x run_vmd_tmp ; \
> > >A A cp run_vmd_tmp "/usr/local/bin"/vmd ; \
> > >A A rm -f run_vmd_tmp
> > >A A echo Make sure "/usr/local/bin"/vmd is in your path.
> > >A A Make sure /usr/local/bin/vmd is in your path.
> > >A A echo "VMD installation complete.AA Enjoy!"
> > >A A VMD installation complete.AA Enjoy!
> > >A A [root_at_localhost src]# vmd
> > >A A /usr/local/lib/vmd/vmd_LINUX: Command not found.
> > >
> > >A A Regards,
> > >
> > >A A Archana
> > >A A On Wed, Nov 23, 2016 at 1:14 PM, John Stone
> > <[1][3]johns_at_ks.uiuc.edu> wrote:
> > >
> > >A A A Hi,
> > >A A A AA Does your CentOS 7 machine have 32-bit runtime
> libraries
> > on it?AA If
> > >A A A not,
> > >A A A you will have to install a 64-bit build instead of a
> 32-bit
> > build.
> > >A A A That could cause the error you're seeing.AA You can
> > double-check whether
> > >A A A that's a likely scenario by checking that
> > /usr/local/lib/vmd/vmd_LINUX
> > >A A A does indeed exist.AA If it does, then most likely your
> > machine lacks
> > >A A A 32-bit
> > >A A A libraries and you'd need to install one of the 64-bit
> builds
> > instead
> > >A A A (LINUXAMD64).
> > >
> > >A A A Cheers,
> > >A A A AA John Stone
> > >A A A AA [2][4]vmd_at_ks.uiuc.edu
> > >A A A On Wed, Nov 23, 2016 at 01:04:45PM +0530, Archana
> > Sonawani-Jagtap wrote:
> > >A A A >AA AA Hi all,
> > >A A A >AA AA I am trying toA installA vmd-1.9.2 on Centos7
> > platform. I have
> > >A A A downloaded
> > >A A A >AA AA theA vmd-1.9.2.bin.LINUX.opengl.tar.gz file.
> > >A A A >AA AA I want to install it in /usr/local, so I
> followed the
> > following
> > >A A A steps:
> > >A A A >
> > >A A A >AA AA 1) I untar it in /usr/local.
> > >A A A >AA AA 2) cd vmd-1.9.2A
> > >A A A >AA AA 3) ./configure
> > >A A A >AA AA 4) cd src
> > >A A A >AA AA 5) make install
> > >A A A >
> > >A A A >AA AA I get following message:
> > >A A A >AA AA Make sure /usr/local/bin/vmd is in your path.
> > >A A A >AA AA VMD installation complete.AAA Enjoy!
> > >A A A >AA AA And when I run vmd from /usr/local/bin, I get
> > following error:
> > >A A A >AA AA /usr/local/lib/vmd/vmd_LINUX: Command not found
> > >A A A >
> > >A A A >AA AA Please help me out
> > >A A A >AA AA Regards,
> > >A A A >AA AA Archana Sonawani-Jagtap
> > >A A A >AA AA S9960791339
> > >
> > >A A A --
> > >A A A NIH Center for Macromolecular Modeling and Bioinformatics
> > >A A A Beckman Institute for Advanced Science and Technology
> > >A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> > >A A A [3][5]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA A
> > Phone: 217-244-3349
> > >A A A [4][6]http://www.ks.uiuc.edu/Research/vmd/
> > >
> > >A A --
> > >A A Archana Sonawani-Jagtap
> > >A A Senior Research Fellow,
> > >A A Biomedical Informatics Centre,
> > >A A NIRRH (ICMR), Parel
> > >A A Mumbai, India.
> > >A A 9960791339
> > >
> > > References
> > >
> > >A A Visible links
> > >A A 1. mailto:[7]johns_at_ks.uiuc.edu
> > >A A 2. mailto:[8]vmd_at_ks.uiuc.edu
> > >A A 3. [9]http://www.ks.uiuc.edu/~johns/
> > >A A 4. [10]http://www.ks.uiuc.edu/Research/vmd/
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [11]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> 217-244-3349
> > [12]http://www.ks.uiuc.edu/Research/vmd/
> >
> > --
> > Archana Sonawani-Jagtap
> > Senior Research Fellow,
> > Biomedical Informatics Centre,
> > NIRRH (ICMR), Parel
> > Mumbai, India.
> > 9960791339
> >
> > References
> >
> > Visible links
> > 1. mailto:johns_at_ks.uiuc.edu
> > 2. mailto:vmd_at_ks.uiuc.edu
> > 3. mailto:johns_at_ks.uiuc.edu
> > 4. mailto:vmd_at_ks.uiuc.edu
> > 5. http://www.ks.uiuc.edu/~johns/A
> > 6. http://www.ks.uiuc.edu/Research/vmd/
> > 7. mailto:johns_at_ks.uiuc.edu
> > 8. mailto:vmd_at_ks.uiuc.edu
> > 9. http://www.ks.uiuc.edu/~johns/
> > 10. http://www.ks.uiuc.edu/Research/vmd/
> > 11. http://www.ks.uiuc.edu/~johns/
> > 12. http://www.ks.uiuc.edu/Research/vmd/
>
> --
> 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/
> 

-- 
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339