[yt-users] yt on kraken

[Andrew Cunningham]

Both the python interpreter and all modules associated with the "module 
load yt/dev" on kraken live on a luster filesytem.  In general I've found 
the kraken luster system to have reasonable bandwidth but high to 
intermittently *extremely high* latency for accessing files.  The yt 
import accesses lots of files and consequently the import from this yt 
installation ranges anywhere from annoyingly slow to unusable.  Compute 
nodes or lightly loaded head nodes are sometimes better, sometimes not it 
seems.

I've install my own build in my home directory on that machine just 
because of this.  Because the home directory is not luster, an install in 
this location can load up normally.  I have not had the yt slow-to-start 
problem since I did this.

The quota on the kraken home directory is too small for the yt installer 
script to download the whole kitchen sink.  However I did manage to 
install the hdf5, h5py, numpy, scipy, matplotlib, setuptools, cython and 
pip packages manually for the kraken system python 2.6 and the latest gcc 
modules.  That did fit in the alloted home space and did finally get all 
the dependencies yt needs working for me.



On Wed, 22 Feb 2012, Britton Smith wrote:

> Hi Nathan,
> 
> It's most likely not hanging, but working on the import.  The filesystem on
> Kraken can be incredibly slow at times.  If you're only waiting a minute or
> so, you will probably need to give it a bit longer.
> 
> Britton
> 
> On Wed, Feb 22, 2012 at 5:15 PM, Nathan Goldbaum <goldbaum at ucolick.org>
> wrote:
>       Hi all,
>
>       I'm trying to run yt on a login node on kraken.  All I'm doing
>       is invoking python from the command line and importing yt.
>        However, python hangs on 'from yt.mods import *'.
>
>       The python interpreter also takes a very long time (~ a minute
>       or so) to start from the command line.
>
>       This happens using both the yt/dev and yt/2.3 module.
>
>       Anyone have any ideas?
>
>       Nathan Goldbaum
>       Graduate Student
>       Astronomy & Astrophysics, UCSC
>       goldbaum at ucolick.org
>       http://www.ucolick.org/~goldbaum
>
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> 
> 
>