[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.

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
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):
                 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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