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Bug #3529

open

memmap error

Added by Scott Stagg about 9 years ago. Updated about 9 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
09/03/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

I got the following error when I tried to make a substack:
... averaging stack for summary web page
Traceback (most recent call last):
File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/alignSubStack.py", line 293, in <module>
subStack.start()
File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/alignSubStack.py", line 279, in start
apStack.averageStack(stack=oldstack,outfile=outavg,partlist=includeParticle)
File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apStack.py", line 328, in averageStack
particles = imagic.read(stack)
File "/panfs/storage.local/imb/stagg/software/myami_dev/pyami/imagic.py", line 73, in read
a = readImagicData(pair['img'], header_dict, frame)
File "/panfs/storage.local/imb/stagg/software/myami_dev/pyami/imagic.py", line 43, in readImagicData
a = numpy.memmap(filename, dtype=dtype, mode='r', offset=start, shape=shape, order='C')
File "/usr/lib64/python2.7/site-packages/numpy/core/memmap.py", line 257, in new
mm = mmap.mmap(fid.fileno(), bytes, access=acc, offset=start)
mmap.error: [Errno 12] Cannot allocate memory

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