[phenixbb] solve won't run.

Andrew Purkiss-Trew andrew.purkiss-trew at cancer.org.uk
Fri Jul 9 03:31:50 PDT 2010

On Thu, 2010-07-08 at 09:41 -0700, Nathaniel Echols wrote:
> On Thu, Jul 8, 2010 at 9:10 AM, <alexander.singer at utoronto.ca> wrote:
>         Hi -- I installed phenix-installer-1.6-289-intel-linux-2.6.tar
>         on my Fedora Core 5 linux partition and most things run -- but
>         not solve (which I was first trying from autosolve).  As
>         recommened by the documentation, when I type phenix.solve,
>         here's what I have ---
>         [root at ausinger oth32_c]# phenix.solve
>         binary=/usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve
>         SOLVEDIR=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files
>         SYMOP=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/symop.lib
>         SYMINFO=/usr/local/phenix-1.6-289/solve_resolve/ext_ref_files/syminfo.lib
>         SOLVE_RESOLVE_MALLOC_MAX=1862380800
>         /usr/local/phenix-1.6-289/build/intel-linux-2.6/solve_resolve/exe/solve: error w hile loading shared libraries: /usr/local/phenix-1.6-289/build/intel-linux-2.6/l ib/libimf.so: cannot restore segment prot after reloc: Permission denied
> This is a conflict with the SE ("Security Enhanced", or some such
> nonsense) Linux extensions.  If you turn these off, SOLVE will run.  I
> don't know the exact instructions, but if you Google for the phrase
> "cannot restore segment prot after reloc: Permission denied", you'll
> find plenty of links.  I think this problem will go away in another
> couple of weeks.

Rather than turning off the SELINUX extensions, you can also fix the
broken permissions. There will be an entry in /var/log/messages telling
you how to trace the error. Googling will also help here.

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