Autosol problem: Failed to carry out Autosol_scale_and_analyze_mad
Dear all I installed phenix nightly builds, dev-256. I have solved structures using molecular replacement. Phenix.refine runs smoothly. Thanks for your great work. When I run some test data using autosol, I met the following error message: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_1_/LAST.LOG) ******************************************************************************** The LAST.LOG appears to be empty. I also run the phenix.solve command. Here is the output: ********************************************************************************************* $ phenix.solve binary=/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=7.48024e+09 /usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied ***************************************************************************************************** The libimf.so file is there. I run phenix.solve as superuser, but I still have the same problem. Thanks for your help. Best, Joe
On Dec 22, 2009, at 5:03 PM, Zheng Zhou wrote:
/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied
Once again, this looks like an SE ("Security Enhanced") Linux problem: http://www.appistry.com/community/forums/content/cannot-restore-segment-prot... or http://www.archiware.com/support/index.php?_m=knowledgebase&_a=viewarticle&kbarticleid=58 and so on (Google has lots more) - the details vary from program to program, but the solution is probably similar regardless of distribution. -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
By the way, what distribution/version of Linux are you using, and do you know if the SE Linux extensions were deliberately turned on or if this was the default? I'd like to add a check for this in the installer so we can warn users - I don't think any of our machines here are set up that way, but we've had several reports of similar problems and it's a relatively obscure error. thanks, Nat On Dec 22, 2009, at 5:03 PM, Zheng Zhou wrote:
Dear all
I installed phenix nightly builds, dev-256. I have solved structures using molecular replacement. Phenix.refine runs smoothly. Thanks for your great work.
When I run some test data using autosol, I met the following error message:
******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad:
None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_1_/LAST.LOG) ********************************************************************************
The LAST.LOG appears to be empty. I also run the phenix.solve command. Here is the output:
********************************************************************************************* $ phenix.solve binary=/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=7.48024e+09
/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied *****************************************************************************************************
The libimf.so file is there. I run phenix.solve as superuser, but I still have the same problem.
Thanks for your help.
Best,
Joe _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Thanks Nat, The temporarily disable worked.
We are using Red Hat Enterprise Linux 5. I think SE Linux is the default.
Best,
Joe
On Tue, Dec 22, 2009 at 8:34 PM, Nathaniel Echols
By the way, what distribution/version of Linux are you using, and do you know if the SE Linux extensions were deliberately turned on or if this was the default? I'd like to add a check for this in the installer so we can warn users - I don't think any of our machines here are set up that way, but we've had several reports of similar problems and it's a relatively obscure error.
thanks, Nat
On Dec 22, 2009, at 5:03 PM, Zheng Zhou wrote:
Dear all
I installed phenix nightly builds, dev-256. I have solved structures using molecular replacement. Phenix.refine runs smoothly. Thanks for your great work.
When I run some test data using autosol, I met the following error message:
******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad:
None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_1_/LAST.LOG) ********************************************************************************
The LAST.LOG appears to be empty. I also run the phenix.solve command. Here is the output:
********************************************************************************************* $ phenix.solve binary=/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve SOLVEDIR=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files SYMOP=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/symop.lib SYMINFO=/usr/local/phenix-dev-254/solve_resolve/ext_ref_files/syminfo.lib CCP4_OPEN=UNKNOWN SOLVE_RESOLVE_MALLOC_MAX=7.48024e+09
/usr/local/phenix-dev-254/build/intel-linux-2.6/solve_resolve/exe/solve: error while loading shared libraries: /usr/local/phenix-dev-254/build/intel-linux-2.6/lib/libimf.so: cannot restore segment prot after reloc: Permission denied *****************************************************************************************************
The libimf.so file is there. I run phenix.solve as superuser, but I still have the same problem.
Thanks for your help.
Best,
Joe _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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Nathaniel Echols -
Zheng Zhou