[yt-users] Memory Error in parallelHF

[Carolyn Peruta]

I'm getting a memory error running parallelHF on Ranger.  Is this a bug or is there some sort of way to request more memory in my job script?

Here is the full traceback:

Traceback (most recent call last):
  File "sim_halo_profiler.py", line 17, in <module>
    rearrange=True, safety=1.5, fancy_padding=True)
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1921, in 
__init__
    threshold=threshold, dm_only=dm_only, rearrange=rearrange, premerge=premerge)
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1368, in 
__init__
    HaloList.__init__(self, data_source, dm_only)
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 992, in _
_init__
    self._run_finder()
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/halo_objects.py", line 1389, in 
_run_finder
    self.threshold, rearrange=self.rearrange, premerge=self.premerge)
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf
ace.py", line 68, in __init__
yt : [INFO     ] 2011-05-13 11:42:17,599 Building kd tree for 9519616 particles...
    self._chain_hop()
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf
ace.py", line 1428, in _chain_hop
    self._chain_hop()
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf
ace.py", line 1428, in _chain_hop
    self._init_kd_tree()
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf
ace.py", line 347, in _init_kd_tree
    fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64'))
    self._init_kd_tree()
  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/yt-2.1stable-py2.6-linux-x86_64.egg/yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interf
ace.py", line 347, in _init_kd_tree
MemoryError    fKD.pos = na.asfortranarray(na.empty((3, self.size), dtype='float64'))

  File "/share/home/01078/tg803421/yt-x86_64/lib/python2.6/site-packages/numpy/core/numeric.py", line 408, in asfortranarray
    return array(a, dtype, copy=False, order='F', ndmin=1)
MemoryError