VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 09 2010 - 21:26:53 CDT

luis,

there is no more general solution outside of using
a proper root shell with su -l. using sudo to install
software is a bad habit that has been inflicted on
people by ubuntu and mac osx for not good reason.

from the administrator's perspectivem the permission
to install software should be given either people with
full root access or done into directories where a specific
user has personal write access. using sudo for these
things is in my opinion as misuse and at best it should
only be tolerated if the sudo shell does _not_ inherit
the user environment but a "clean" environment (hence
the su -l and not plain su).

for most people that don't have full root access, installing
VMD into some directory under $HOME and placing the
vmd launch script into $HOME/bin works just as well and
is probably what you should have done in the first place.

sorry for the direct words, but these things should not
happen in my opinion...

cheers,
    axel.

On Wed, Jun 9, 2010 at 7:35 PM, Luis Guillermo Cota Preciado
<lgcota_at_gmail.com> wrote:
> 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
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.