[yt-users] Problem with common unstable branch on Kraken

Matthew Turk matthewturk at gmail.com
Wed May 25 12:10:17 PDT 2011


Hi all,

If we are able to track this down to an item that's not in yt -- i.e.,
an interplay between h5py, numpy, python 2.7, etc -- we should try to
report these issues upstream.  In the past there have been indications
that interplay between Python 2.7 and h5py 1.3.1 have caused issues,
although this particular issue is unfamiliar to me.  h5py 1.4.0 is
coming out soon (a beta was just released) so perhaps there will be
relief on that end.

Anyway, if you can figure out how to get this problem to be reproduced
without importing yt directly, it might help track it down.

Also, Geoffrey, I think I have run on up to 64 processors on Nautilus,
but maybe not since the latest upgrade.  Thanks for the pointer about
mpt and the neighborhood issue.

Best,

Matt

On Wed, May 25, 2011 at 3:06 PM,  <gso at physics.ucsd.edu> wrote:
> I'm not sure if this is relevant to Kraken users, but I have gone through
> a lot of trouble to make YT work on Nautilus, which is similar machine to
> Kraken.  After going back and forth with the sys admins, I was told to do
> the following:
>
> module swap mpt mpt/2.03
> export MPI_SHARED_NEIGHBORHOOD=HOST
>
> and use no more than 8 cores due to some bug in the drivers of a
> particular hardware.
>
> Once I had YT working on Nautilus I haven't tried to use YT on Kraken.
>
> From
> G.S.
>
>> I encountered a similar error trying to run python 2.7 in parallel on
>> kraken.  Has anyone on this list been able to the Kraken YT install in
>> parallel?  If anyone has, it would be vary helpful to know.
>>
>> Britton
>>
>> On Wed, May 25, 2011 at 12:57 PM, Anthony Harness <
>> anthony.harness at colorado.edu> wrote:
>>
>>> Using the "unstable" version of yt on Kraken, I get the following error
>>> while simply trying to import yt while running in parallel. I haven't
>>> done
>>> anything memory-intensive, so I suspect this is a bug. I have the
>>> PrgEnv-gnu
>>> module loaded.
>>>
>>>
>>> Traceback (most recent call last):
>>>   File "/lustre/scratch/harnessa/analysis/Clumping/test2.py", line 1, in
>>> <module>
>>>     from yt.mods import *
>>>   File
>>> "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/yt-2.2dev-py2.7-linux-x86_64.egg/yt/mods.py",
>>> line 35, in <module>
>>>     import numpy as na # For historical reasons
>>>   File
>>> "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/numpy/__init__.py",
>>> line 154, in <module>
>>>     import ctypeslib
>>>   File
>>> "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/numpy/ctypeslib.py",
>>> line 60, in <module>
>>>     import ctypes
>>>   File
>>> "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/ctypes/__init__.py",
>>> line 549, in <module>
>>>     CFUNCTYPE(c_int)(lambda: None)
>>> MemoryError
>>>
>>>
>>> Thanks,
>>> Anthony
>>>
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