[phenixbb] v1.8 bug ? memory allocation crash in map calculation (phenix.refine, phenix.maps)
Phil Jeffrey
pjeffrey at princeton.edu
Tue Jul 10 14:46:05 PDT 2012
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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