[yt-users] yt on kraken

[Patel, Pragneshkumar B]

Hi Nathan,

> Would it be impossible to install the yt module on an NFS filesystem?  I gather that Hari Krishnan reads this user list, maybe he can weigh in on some best practices for using the yt 
> module on Kraken.

It is possible to install the yt on NFS. But you can not access it from compute nodes. You can only use it on login nodes.  

Pragnesh



On Feb 22, 2012, at 4:40 PM, Andrew Cunningham wrote:

> 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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>>
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