[phenixbb] phenix error?

Randy Read rjr27 at cam.ac.uk
Mon Sep 28 10:39:42 PDT 2009

Dear Venkat,

Could you try this with the latest nightly build?  We've just fixed a  
bug in the anisotropy correction in Phaser (which is the part where  
the error was triggered).  The bug crept in sometime in August and was  
just fixed on Friday.

If this doesn't fix the problem, then perhaps you could send me the  
data (offline) and I could try to reproduce the problem.

Best wishes,

Randy Read

On 28 Sep 2009, at 18:04, r n wrote:

> Hi all
> I have come across a new error while running the phenix.automr as  
> follows, it works
> fine untill last week? Not sure what causes this error.
> :Output&, TNT::Vector<double>, double, TNT::Vector<double>,  
> TNT::Vector<double>&, double, double, double, bool&, bool&)+0x1bf0)  
> [0x2aaab34594b0]
>   /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel- 
> linux-2.6-x86_64/lib/ 
> phaser_ext.so(phaser::Minimizer::ShiftScore(double,  
> phaser::RefineBase&, TNT::Vector<double>&, TNT::Vector<double>&,  
> TNT::Vector<double>&, phaser::Output*, bool)+0x45) [0x2aaab3457845]
>   /home/pgm/phenix-installer-1.4-147/phenix-1.4-147/build/intel- 
> linux-2.6-x86_64/lib/phaser_ext.so(phaser::RefineANO::targetFn() 
> +0x1a4) [0x2aaab34d9054]
>   /lib64/libc.so.6 [0x3e6c830070]
> Floating-point error (Python and libc call stacks above)
>                 This crash may be due to a problem in any imported
>                 Python module, including modules which are not part
>                 of the cctbx project. To disable the traps leading
>                 to this message, define these environment variables
>                 (e.g. assign the value 1):
>                     BOOST_ADAPTBX_FPE_DEFAULT
>                 This will NOT solve the problem, just mask it, but
>                 may allow you to proceed in case it is not critical.
> any help?
> Thanks
> venkat
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www- 

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