[phenixbb] v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)

Nathaniel Echols nechols at lbl.gov
Tue Jul 10 14:49:15 PDT 2012


Try turning off the filling of missing F-obs (fill_missing_f_obs=False).

On Tue, Jul 10, 2012 at 2:46 PM, Phil Jeffrey <pjeffrey at princeton.edu> wrote:
> This is in F432 in a=b=c=340A at 2.85A resolution.  Mac OSX 10.5.8, the
> machine has 8Gb memory of which something like 6Gb is hanging around begging
> to be used.
>
> 1,327,104,000 if that's in bytes doesn't seem all that excessive.
> On the other hand, 340*340*340= 39,419,600 so it's perhaps a little greedy.
>
> Limits set by shell:
> phil% limit
> cputime      unlimited
> filesize     unlimited
> datasize     unlimited
> stacksize    65532 kbytes
> coredumpsize 0 kbytes
> memoryuse    unlimited
> descriptors  256
> memorylocked unlimited
> maxproc      266
>
>
> phenix.refine does the same thing right at the end, which is kind of a shame
> since it takes quite a long time to run.  phenix.maps does the same thing
> even if I ask it just to generate F,phase in MTZ format.
>
>
> [snip]
> Compute maps.
> Python(632) malloc: *** mmap(size=1327104000) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> show_stack(1):
> /usr/local/phenix-1.8-1069/cctbx_project/cctbx/miller/__init__.py(3067)
> double_step_filtration
> show_stack(2):
> /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(416)
> map_coefficients_from_fmodel
> show_stack(3):
> /usr/local/phenix-1.8-1069/cctbx_project/mmtbx/maps/__init__.py(543)
> __init__
> show_stack(4):
> /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(325)
> run
> show_stack(5):
> /usr/local/phenix-1.8-1069/build/mac-intel-osx/../../cctbx_project/mmtbx/command_line/maps.py(402)
> <module>
> Bus error (Python call stack 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
>                     BOOST_ADAPTBX_SIGNALS_DEFAULT
>                 This will NOT solve the problem, just mask it, but
>                 may allow you to proceed in case it is not critical.
>
>
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