VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 04 2006 - 11:28:38 CDT

Hi,
  Indeed, my understanding from browsing the web is that the default
FC5 SELinux settings break essentially everything that uses plugins,
including web browsers, and VMD, as setup out of the box.

If you don't want to disable SELinux entirely, I suggest you try
running this command on the VMD installation directory (Assumes the
VMD directory is local to the machine... If you're mounting over NFS,
this may or may not work. If not, then you may have to disable SELinux
as described below)
  cd /usr/local/lib/vmd
  find . -name \*.so -exec chcon -t texrel_shlib_t {} \;

If you'd rather just turn SELinux off, try setting the line:
  SELINUX=disabled
in your /etc/sysconfig/selinux and then reboot the machine.

One of those two options ought to solve the problem in the short term.

Redhat has modified the C/C++ compilers and linkers shipping with
FC5 to produce executables and shared libraries that conform to the
SELinux requirements. Programs (like VMD) that are compiled on an older
or different Linux version can't use these new flags, so the result is that
SELinux blocks them until you make an exception for them.
For VMD 1.8.4, I'm going to ship Linux executables built the normal way.
I'll be looking into using the new SELinux related "-fpie" flags in builds
of future versions of VMD, which should hopefully eliminate this SELinux
relocatable .so file fiasco.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 04, 2006 at 09:04:43AM +0200, Eugen Leitl wrote:
> On Tue, Apr 04, 2006 at 12:18:22AM -0500, snoze pa wrote:
> > after upgrading to Fedora core 5, I am getting following error message
> > in VMD. Any idea about this error message
> >
> > package require solvate
> > couldn't load file
> > "/usr/local/lib/vmd/plugins/LINUX/tcl/psfgen1.4/libpsfgen.so":
> > /usr/local/lib/vmd/plugins/LINUX/tcl/psfgen1.4/libpsfgen.so: cannot
> > restore segment prot after reloc: Permission denied
>
> Try turning SELinux off, and rebooting.
>
> --
> Eugen* Leitl leitl http://leitl.org
> ______________________________________________________________
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-- 
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