[phenixbb] Autosol problem: Failed to carry out Autosol_scale_and_analyze_mad

Zheng Zhou zhengzhouzz at gmail.com
Tue Dec 22 23:45:13 PST 2009


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 <NEchols at lbl.gov> wrote:
> 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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>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
> --------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
>
>
>
>
>
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>



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