VMD-L Mailing List

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Thu Nov 24 2016 - 09:34:11 CST

Hi,

I think you are using your cluster resource, and trying to install vmd on your cluster.

Therefore, I think you dont have permission to install vmd to server home. In this case or not, try the following the steps. I am sure you will be able to install the vmd successfully, I am also using vmd on centOS.

Try this:

1. Make three folders xyz, bin and lib inside one folder for example abc.

- it should look like this:

 -cd abc

 -ls abc (in this folder you find three folders as follows)

 -xyz lib bin (these three)

2. You have vmd tar file in this folder "xyz".

 -cd xyz

 -tar xvf vmd.tar.gz

 -cd vmd

 -vi configure

this will open the configure file, now change the usr/local/bin and usr/local/lib as follows:

# Name of shell script used to start program; this is the name used by users

$install_name = "vmd";

# Directory where VMD startup script is installed, should be in users' paths.

$install_bin_dir="/home/abc/bin";

# Directory where VMD files and executables are installed

$install_library_dir="/home/abc/lib/$install_name";

(here "home" folder is your folder home; you can type "pwd" to get the path of home or just remove home)

3. now just easy to follow the steps:

- ./configure LINUXAMD

- cd src

- make install

 thik will hep you to install vmd.

best

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Archana Sonawani-Jagtap <ask.archana_at_gmail.com>
Sent: Thursday, November 24, 2016 4:56:44 PM
To: John Stone; Archana Sonawani-Jagtap; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: vmd installation

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 <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
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<mailto: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<mailto: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<mailto: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<mailto:johns_at_ks.uiuc.edu>
> 2. mailto:vmd_at_ks.uiuc.edu<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/
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339