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Bug #1435

closed

mrc can not read large stack even with memory mapping

Added by Anchi Cheng about 13 years ago. Updated over 11 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Jim Pulokas
Category:
Python scripting
Target version:
Appion/Leginon 3.0.0
Start date:
09/28/2011
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

try:/ami/data00/ami/data00/appion/11sep14d/ddstack/ddraw1/11sep14d_00010sq_v01_00003hl_v01_00002ed_st.mrc
The stack is 4096x3072x60

got
Warning: overflow encountered in long_scalars
Traceback (most recent call last):
File "updateStackHeader.py", line 27, in ?
updateHeaderStats(stackpath,-1)
File "updateStackHeader.py", line 14, in updateHeaderStats
a = mrc.mmap(filepath)
File "/home/acheng/myami/pyami/mrc.py", line 695, in mmap
mrcdata = numpy.memmap(filename, dtype=headerdict['dtype'], mode='r', offset=1024, shape=headerdict['shape'], order='C')
File "/usr/lib/python2.4/site-packages/numpy/core/memmap.py", line 67, in new
mm = mmap.mmap(fid.fileno(), bytes, access=acc)
OverflowError: memory mapped size must be positive

Also tried mrc.read() and got
754974720 items requested but only 0 read
Segmentation fault

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