VMD-L Mailing List

From: Luis Guillermo Cota Preciado (lgcota_at_gmail.com)
Date: Wed Jun 09 2010 - 18:35:18 CDT

John,

It worked, thanks. I look forward to the more general solution.

Regards.

2010/6/9 John Stone <johns_at_ks.uiuc.edu>

>
> 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
>