VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 09 2010 - 16:17:18 CDT

Hi,
  From the permissions you're getting, I conclude that when you install
with sudo, your umask is causing the copy/tar commands to create files
with permissions that are more restrictive than what we'd normally want.

Try doing this to your installed VMD tree and see if it cures your problems
or not (this is a bit excessive to be sure, but I just want to see if your
problems are all entirely permission related):
  chmod -R 755 /usr/local/lib/vmd

I could do various things to the install scripts to force permissions to
be preserved on installs, but this can create problems with some
implementations of tar I've run across, so I'm a bit leery to change
the behavior presently. I'll look into what might be a better solution
for cases like yours.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 07, 2010 at 12:17:58AM -0500, Luis Guillermo Cota Preciado wrote:
> John,
> It does, thanks. However, I can't get it to appear during the startup if I
> liberalize the permission strings even more. In order to rule out some
> previous mistake of mine I deleted VMD and reinstalled it only to end up
> with the same things:
> 1) When I follow the installation instructions from the README I can't
> install on the default locations
> (obviously so because it is in the realm of the superuser.)
> 2) When I toss in sudo or su I do get the installation, but no exec
> permissions for the lowly user. Tweaking vmd_LINUX's to o+x is enough to
> get VMD going, but not to display the main menu. Permissions for other
> files seem to be correct:
> -rw-r--r-- 1 root root 2020 2010-06-06 23:34 Announcement
> drwxr-xr-x 2 root root 72 2010-06-04 01:24 doc
> -rwxr-x--- 1 lgc lgc 246044 2009-05-11 12:54 libcudart.so.2
> -rw-r--r-- 1 root root 7753 2010-06-06 23:34 LICENSE
> drwxr-x--- 5 lgc lgc 120 2009-08-01 01:44 plugins
> -rw-r--r-- 1 root root 14964 2010-06-06 23:34 README
> drwxr-x--- 8 lgc lgc 216 2009-08-01 01:44 scripts
> drwxr-x--- 3 lgc lgc 184 2009-08-01 01:41 shaders
> -rwxr-xr-x 1 root root 1167079 2010-06-06 23:34 stride_LINUX
> -rwxr-xr-x 1 root root 352948 2010-06-06 23:34 surf_LINUX
> -rwxr-xr-x 1 root root 176272 2010-06-06 23:34 tachyon_LINUX
> -rw-r--r-- 1 root root 3166 2010-06-06 23:34 vmd_completion.dat
> -rwxr-x--x 1 root root 5921104 2010-06-06 23:34 vmd_LINUX,
> (lgc is yours truly). My umask is 0027.
> Apart from the possibility that I'm doing something wrong, in which case I
> would like to know further, it seems to me that either the configure
> script needs to be modified in order to take care of permissions issues
> and proper mention be made to the use of "su" or "sudo" on the README, or
> the default install should take place in the current directory without
> modifying the configure script.
> Thanks.
>
> 2010/6/4 John Stone <johns_at_ks.uiuc.edu>
>
> Luis,
> Does the main menu open when you type this command?:
> menu main on
>
> If so, then it must be more permissions issues caused by
> the behavior of sudo and the resulting file umask on your machine.
>
> If not, then tell me what this command says:
> vmdinfo options
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 04, 2010 at 10:19:01AM -0500, Luis Guillermo Cota Preciado
> wrote:
> > Hi John,
> > There seems to be no .vmdinit file anywhere. The .vmdrc file that
> sits in
> > /usr/local/lib/vmd is not empty, and there is no such file in my
> $HOME.
> > Here's the ls -al dump of /usr/local/lib/vmd:
> > drwxr-xr-x 6 root root 480 2010-06-04 01:24 .
> > drwxr-xr-x 10 root root 272 2010-06-04 01:24 ..
> > -rw-r--r-- 1 root root 2020 2010-06-04 01:24 Announcement
> > drwxr-xr-x 2 root root 72 2010-06-04 01:24 doc
> > -rwxr-xr-- 1 lgc lgc 246044 2009-05-11 12:54 libcudart.so.2
> > -rw-r--r-- 1 root root 7753 2010-06-04 01:24 LICENSE
> > drwxr-xr-- 5 lgc lgc 120 2009-08-01 01:44 plugins
> > -rw-r--r-- 1 root root 14964 2010-06-04 01:24 README
> > drwxr-xr-- 8 lgc lgc 216 2010-06-04 01:24 scripts
> > drwxr-xr-- 3 lgc lgc 184 2009-08-01 01:41 shaders
> > -rwxr-xr-x 1 root root 1167079 2010-06-04 01:24 stride_LINUX
> > -rwxr-xr-x 1 root root 352948 2010-06-04 01:24 surf_LINUX
> > -rwxr-xr-x 1 root root 176272 2010-06-04 01:24 tachyon_LINUX
> > -rw-r--r-- 1 root root 3166 2010-06-04 01:24 vmd_completion.dat
> > -rwxr-xr-x 1 root root 5921104 2010-06-04 01:24 vmd_LINUX
> > -rw-r----- 1 root root 1813 2010-06-04 01:24 .vmdrc
> > -rw-r----- 1 root root 1784 2010-06-04 01:24 .vmdsensors
> > Thank you for your help.
> > 2010/6/4 John Stone <johns_at_ks.uiuc.edu>
> >
> > Hi,
> > Did you verify that the .vmdinit file in the installation
> > directory is readable by a normal user? You might also check
> > that you don't have an empty .vmdrc sitting around in your
> > home directory. If neither of those is the problem, send me
> > the 'ls -al' output on your installation directory and I'll have
> > a quick look.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> > On Fri, Jun 04, 2010 at 02:32:23AM -0500, Luis Guillermo Cota
> Preciado
> > wrote:
> > > Hi,
> > > I followed the instructions within the README file, to no
> avail,
> > trying to
> > > do a default installation. I had to -but of course!- use
> sudo in
> > order to
> > > proceed without errors. However, I ended up with no
> permissions for
> > the
> > > normal user, which I had to tweak by hand in order to get
> VMD
> > running.
> > > However, somehow the otherwise usual "main" window (whatever
> its
> > name is),
> > > the one for loading and displaying and all that, is absent.
> Just
> > the
> > > terminal and the visualization area are present.
> > > What gives? Thanks.
> >
> > --
> > 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
>
> --
> 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 

-- 
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