[phenixbb] fem command/memory error

Pavel Afonine pafonine at lbl.gov
Wed May 14 07:37:21 PDT 2014


Hi Matteo,

I'm sorry about the problem!

I afraid there are only solution two solutions: 1) use a computer with 
more memory: the error below tells the program needed more memory than 
your computer has, or 2) wait for a one of upcoming nightly builds.

Since the release I've already made a number of changes that should help 
free some memory: for example, I switched from 1/4. to 1/3 gridding, 
which should significantly reduce the memory consumption (and speed up 
the calculations too).

Pavel

On 5/14/14, 1:44 AM, Matteo Colombo wrote:
> Hi Pavel,
> I downloaded the last released version of phenix (phenix-1.9-1692) and 
> I would like to run the "feature enhanced map" command.
>
> However, when I run it I got the following Memory Error that I didn't 
> have in the previous version of phenix.
>
> r_work: 0.1867 r_free: 0.2372
> Max B subtracted from atoms and used to sharpen map: 20.0
> b_sharp: 25.0
> FEM loop: done so far: 10%Traceback (most recent call last):
>   File 
> "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", 
> line 120, in <module>
>     run(sys.argv[1:])
>   File 
> "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", 
> line 99, in run
>     sharp=params.sharp, signal_threshold=params.signal_threshold)
>   File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", 
> line 112, in __init__
>     progress_counter = progress_counter)
>   File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", 
> line 204, in fem_loop
>     weighted_average_manager    = weighted_average_manager)
>   File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", 
> line 276, in fem_loop_
>     weighted_average_manager = weighted_average_manager)
>   File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", 
> line 234, in one_iteration
>     m = get_map(mc=mc_wa, cg=crystal_gridding)
>   File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", 
> line 20, in get_map
>     fourier_coefficients = mc)
>   File 
> "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", 
> line 4357, in __init__
>     conjugate_flag=True)
> MemoryError
>
>
> My OS is Ubuntu precise 12.04 LTS, system 32 bit
>
>
> Thanks in advance
>
> Matteo
>
> -- 
> Matteo Colombo PhD
> Groupe Extremophile et grands assemblages moléculaire
> Institut de Biologie Structural J. P. Ebel
> 6, rue Jules Horowitz
> F-38027 GRENOBLE Cedex 1
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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