VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 24 2016 - 01:32:23 CST

Hi,
  I think you misunderstood about the approach to installing the
64-bit version. 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). 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,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 24, 2016 at 12:42:42PM +0530, Archana Sonawani-Jagtap wrote:
> Hi,
>
> I tried ./configure LINUXAMD64, but still I get the following after make
> install:
>
> if [ ! -d "/usr/local/lib/vmd" ]; then \
> A A A mkdir -p "/usr/local/lib/vmd" ; \
> fi ; \
> if [ ! -d "/usr/local/bin" ]; then \
> A A A mkdir -p "/usr/local/bin" ; \
> fi ; \
> if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
> A A A mkdir -p "/usr/local/lib/vmd"/doc; \
> fi
> cp ../AnnouncementA "/usr/local/lib/vmd"
> cp ../READMEA A A A A A A "/usr/local/lib/vmd"
> cp ../LICENSEA A A A A A "/usr/local/lib/vmd"
> cp ../doc/ug.pdfA A A A A A A "/usr/local/lib/vmd"/doc
> if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
> A A A A A A A A A A mv -f "/usr/local/lib/vmd/vmd_LINUXAMD64"
> "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; rm -f
> "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
> cp ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
> cp: cannot stat a**../LINUXAMD64/vmd_LINUXAMD64a**: No such file or
> directory
> make: [install] Error 1 (ignored)
> if [ -d "../lib/redistrib/lib_LINUXAMD64" ]; then \
> A A A cd ../lib/redistrib/lib_LINUXAMD64; tar -cf - ./* | \
> A A A (cd "/usr/local/lib/vmd" ; tar -xf -) \
> fi ;
> cp ../lib/stride/stride_LINUXAMD64 ../lib/surf/surf_LINUXAMD64
> ../lib/tachyon/tachyon_LINUXAMD64 "/usr/local/lib/vmd"
> cp: cannot stat a**../lib/stride/stride_LINUXAMD64a**: No such file or
> directory
> cp: cannot stat a**../lib/surf/surf_LINUXAMD64a**: No such file or
> directory
> cp: cannot stat a**../lib/tachyon/tachyon_LINUXAMD64a**: No such file or
> directory
> make: [install] Error 1 (ignored)
> cd ..; tar -cf - scripts | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ../lib; tar -cf - scripts | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ..; tar -cf - python | \
> (cd "/usr/local/lib/vmd"/scripts ; tar -xf -)
> cd ..; tar -cf - plugins | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> cd ..; tar -cf - shaders | \
> (cd "/usr/local/lib/vmd" ; tar -xf -)
> if [ -f ../LINUXAMD64/OptiXShaders.ptx ]; then \
> A A A cp ../LINUXAMD64/OptiXShaders.ptx "/usr/local/lib/vmd/shaders"; \
> fi;
> cp ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat
> "/usr/local/lib/vmd"
> cd ../bin ; \
> if [ -f run_vmd_tmp ]; then rm -f run_vmd_tmp; fi ; \
> if [ ! -x "/bin/csh" ]; then \
> A A A echo "Info: /bin/csh shell not found, installing Bourne shell
> startup script instead" ; \
> A A A echo '#!/bin/sh' >> run_vmd_tmp ; \
> A A A echo 'defaultvmddir="/usr/local/lib/vmd"' >> run_vmd_tmp ; \
> A A A echo 'vmdbasename=vmd' >> run_vmd_tmp ; \
> A A A cat vmd.sh >> run_vmd_tmp ; \
> else \
> A A A echo '#!/bin/csh' >> run_vmd_tmp ; \
> A A A echo 'set defaultvmddir="/usr/local/lib/vmd"' >> run_vmd_tmp ; \
> A A A echo 'set vmdbasename=vmd' >> run_vmd_tmp ; \
> A A A cat vmd.csh >> run_vmd_tmp ; \
> fi ; \
> chmod +x run_vmd_tmp ; \
> cp run_vmd_tmp "/usr/local/bin"/vmd ; \
> rm -f run_vmd_tmp
> echo Make sure "/usr/local/bin"/vmd is in your path.
> Make sure /usr/local/bin/vmd is in your path.
> echo "VMD installation complete.A Enjoy!"
> VMD installation complete.A Enjoy!
> [root_at_localhost src]# vmd
> /usr/local/lib/vmd/vmd_LINUX: Command not found.
>
> Regards,
>
> Archana
> On Wed, Nov 23, 2016 at 1:14 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> A Does your CentOS 7 machine have 32-bit runtime libraries on it?A If
> not,
> you will have to install a 64-bit build instead of a 32-bit build.
> That could cause the error you're seeing.A You can double-check whether
> that's a likely scenario by checking that /usr/local/lib/vmd/vmd_LINUX
> does indeed exist.A If it does, then most likely your machine lacks
> 32-bit
> libraries and you'd need to install one of the 64-bit builds instead
> (LINUXAMD64).
>
> Cheers,
> A John Stone
> A [2]vmd_at_ks.uiuc.edu
> On Wed, Nov 23, 2016 at 01:04:45PM +0530, Archana Sonawani-Jagtap wrote:
> >A A Hi all,
> >A A I am trying toA installA vmd-1.9.2 on Centos7 platform. I have
> downloaded
> >A A theA vmd-1.9.2.bin.LINUX.opengl.tar.gz file.
> >A A I want to install it in /usr/local, so I followed the following
> steps:
> >
> >A A 1) I untar it in /usr/local.
> >A A 2) cd vmd-1.9.2A
> >A A 3) ./configure
> >A A 4) cd src
> >A A 5) make install
> >
> >A A I get following message:
> >A A Make sure /usr/local/bin/vmd is in your path.
> >A A VMD installation complete.AA Enjoy!
> >A A And when I run vmd from /usr/local/bin, I get following error:
> >A A /usr/local/lib/vmd/vmd_LINUX: Command not found
> >
> >A A Please help me out
> >A A Regards,
> >A A Archana Sonawani-Jagtap
> >A A S9960791339
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/A A A A A A Phone: 217-244-3349
> [4]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. http://www.ks.uiuc.edu/~johns/
> 4. 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/