Appion

Hi Scott, no it only loads images to fill the viewer. I have tried this on 10GB stacks.

I guess it would have to load all the classified particles to do PCA. But this was a big concern of mine.

Can you provide more info, does it crash on load?

I get a memory error on one machine

[sstagg@hpc-login-34 ~]$ runLearnStackCleaner.py --stack-id=291 --commit --rundir=/lustre/cryo/lustre/appiondata/16sep07b/stacks/learn291 --runname=learn291 --projectid=1 --expid=11581 --jobtype=makestack

 ... Time stamp: 16oct07n28
 ... Function name: runLearnStackCleaner
 ... Appion directory: /panfs/storage.local/imb/stagg/software/myamiss/appion
 ... Processing hostname: hpc-login-34.rcc.fsu.edu
 ... Using split database
Connected to database: 'ap1'
 ... Committing data to database
 ... Run directory: /lustre/cryo/lustre/appiondata/16sep07b/stacks/learn291
!!! WARNING: directory '/lustre/cryo/lustre/appiondata/16sep07b/stacks/learn291' already exists.
 ... Writing function log to: runLearnStackCleaner.log
 ... Uploading ScriptData....
 ... Found 24 processors on this machine
 ... Running Appion version 'trunk'
!!! WARNING: Assuming apix is 1.0 A/pixel
Traceback (most recent call last):
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/bin/runLearnStackCleaner.py", line 135, in <module>
    learnstack.start()
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/bin/runLearnStackCleaner.py", line 68, in start
    a.run()
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/proc2dLib.py", line 78, in run
    self.approc2d.start()
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/proc2dLib.py", line 405, in start
    indata = self.readFileData(self.params['infile'])
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/proc2dLib.py", line 228, in readFileData
    data = imagic.read(filename)
  File "/panfs/storage.local/imb/stagg/software/myamiss/pyami/imagic.py", line 73, in read
    a = readImagicData(pair['img'], header_dict, frame)
  File "/panfs/storage.local/imb/stagg/software/myamiss/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

I can launch it on a high memory machine, but it take up a big chunk when it is starting up but then it goes down.