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alexander.singer＠utoronto.ca

8 Jul 2010 8 Jul '10

4:10 p.m.

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@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 CCP4_OPEN=UNKNOWN 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 Do you know what I can do about this? Thanks Alex -- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

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Tom Terwilliger

8 Jul 8 Jul

4:41 p.m.

Hi Alex, Try this: you need to be root edit /etc/sysconfig/selinux: SELINUX=disabled then reboot. Let me know if this doesn't do it. All the best, Tom T On Jul 8, 2010, at 10:10 AM, [email protected] 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@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 CCP4_OPEN=UNKNOWN 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

Do you know what I can do about this?

Thanks

Alex

-- Dr. Alex Singer C.H. Best Institute 112 College St. Room 70 University of Toronto Toronto, Canada, M5G 1L6 416-978-4033

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

Nathaniel Echols

4:41 p.m.

On Thu, Jul 8, 2010 at 9:10 AM, 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@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 CCP4_OPEN=UNKNOWN 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. PS. Please update to version 1.6.2. -Nat

Andrew Purkiss-Trew

9 Jul 9 Jul

10:31 a.m.

On Thu, 2010-07-08 at 09:41 -0700, Nathaniel Echols wrote:

...

On Thu, Jul 8, 2010 at 9:10 AM, 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@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 CCP4_OPEN=UNKNOWN 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. This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

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