[phenixbb] Autosol problem: Failed to carry out Autosol_scale_and_analyze_mad

[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
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--------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov