[Yt-dev] nickel instruction for using parallel HOP (not on Kraken)

Britton Smith brittonsmith at gmail.com
Tue Dec 1 09:25:12 PST 2009


Hi Stephen,

I'm having a problem with parallelHOP where one (and seemingly only one) of
the processors is having an array out of bounds error with the
densest_in_chain_real_index array.  I printed out the size of this array and
the densest_in_chain array and in the one processor where it fails the
densest_in_chain_real_index array has one less element.  Below is the
traceback:

The three numbers printed out at the top are the sizes of densest_in_chain,
densest_in_chain_real_index, and sort, in that order.

P005 yt         INFO       2009-12-01 10:12:28,438 Locally sorting chains...
3794
3793
3794
Traceback (most recent call last):
  File "do_hop.py", line 9, in <module>
    fancy_padding=True, rearrange=True)
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/HaloFinding.py",
line 958, in __init__
    threshold=threshold, dm_only=dm_only, rearrange=rearrange)
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/HaloFinding.py",
line 598, in __init__
    HaloList.__init__(self, data_source, dm_only)
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/HaloFinding.py",
line 339, in __init__
    self._run_finder()
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/HaloFinding.py",
line 609, in _run_finder
    self.threshold, rearrange=self.rearrange)
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/parallelHOP/parallelHOP.py",line
56, in __init__
    self._chain_hop()
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/parallelHOP/parallelHOP.py",line
1423, in _chain_hop
    chain_count = self._preconnect_chains(chain_count)
  File
"/duanestorage/home/student/brittons/local/x86_64/lib/python2.6/site-packages/yt-1.6dev-py2.6-linux-x86_64.egg/yt/lagos/parallelHOP/parallelHOP.py",line
538, in _preconnect_chains
    self.densest_in_chain_real_index =
self.densest_in_chain_real_index[sort]
IndexError: index 3793 out of bounds 0<=index<3793

Do you have any idea what's going on here?

Thanks,
Britton

On Wed, Nov 25, 2009 at 4:45 PM, Stephen Skory <stephenskory at yahoo.com>wrote:

> J. S.,
>
>
> > > 2. Install Forthon in the standard python way.
> > > http://hifweb.lbl.gov/Forthon/
> > Can I ask what made you use Forthon over f2py? I have been using f2py,
> > and have found it quite useful for wrapping fortran code. Given that
> > f2py comes with numpy, I'm wondering what the specific advantage for
> > Forthon is, if any.
>
> I was unable to convince f2py to build static objects, which is required on
> Kraken. That is it's big advantage.
>
>  _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ <http://physics.ucsd.edu/%7Esskory/> _.>/
> _Graduate Student
> ________________________________(_)_\(_)_______________
> _______________________________________________
> Yt-dev mailing list
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>
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