[yt-dev] memory usage with --parallel and periodic radius

[Nathan Goldbaum]

Hi Mike,

Sorry to hear you're having issues with my changes.  Just to justify myself
a little bit: the old way of generating the radius field silently produced
incorrect results on non-periodic datasets.  yt is increasingly being used
to examine these datasets and I wanted to make sure that the results of a
simple radial profile analysis would be correct.

That being said, the memory consumption is clearly not as good now.  When I
wrote the new code to handle the radius fields, I didn't realize that the
Radius field was so intimately tied to halo finding.

A quick fix to allow you to continue doing your analyses would be to
replace the Radius field with the old definition.  This can be done without
committing any changes to the yt codebase by using the my_plugins.py file.
 Just create a file called my_plugins.py, place it in the .yt folder that
lives in your home directory, and enter the old Radius and ParticleRadius
field definitions inside of it.  I've pasted an example my_plugins.py file
that does this here: http://paste.yt-project.org/show/3212/

Fields defined in my_plugins.py will override definitions in
universal_fields.py, so if the new field definitions are the primary cause
of the increased memory consumption you're seeing, this should fix it.

This isn't a very good long term solution and I'd like to work with you and
others who deal with large datasets to find a permanent solution.  A good
first step would be to file an issue about this.  I don't have a lot of
experience working with large datasets so any help figuring out how to
reduce the memory needs of the Radius field would be appreciated.

Cheers,

Nathan


On Wed, Feb 27, 2013 at 8:01 PM, Michael Kuhlen <mqk at astro.berkeley.edu>wrote:

> > With the last good changeset the total memory usage never gets above
> ~8.5GB (estimated from top).
>
> Sorry, forgot to say: the last good changeset is 41358eecdad5.
>
>
> On Wed, Feb 27, 2013 at 7:58 PM, Michael Kuhlen <mqk at astro.berkeley.edu>wrote:
>
>> Hi all and Nathan specifically
>>
>> I've found that the changes having to do with periodic fields are causing
>> excessive memory usage for me when doing parallel halo profiling, to the
>> point where I can no longer do analysis that used to work fine on my 24GB
>> memory workstation.
>>
>> A simple HaloProfiler script (http://paste.yt-project.org/show/3211/),
>> run in parallel on 8 processors on the halo catalog obtained from one of my
>> cosmology simulations, currently almost immediate runs out of memory, while
>> it used to complete without problems.
>>
>> I tried to use hg bisect to find the problematic changeset but had to
>> skip the testing of several revisions because of runtime yt errors, so in
>> the end bisect only gave me a range of potentially bad revisions:
>> http://paste.yt-project.org/show/3210/. As you can see, they're all
>> related to the periodic radius mods from about a month ago.
>>
>> I tried replicating this with the standard Enzo_64 example dataset from
>> http://yt-project.org/data/, but I guess that one is too small to
>> produce this problem on my machine. If you want to see the problem for
>> yourself, then you can download this tarball (
>> http://astro.berkeley.edu/~mqk/transfer/RD0003.tar 4.5GB) and run this
>> script (http://paste.yt-project.org/show/3211/) on it, like so:
>>
>> $ mpirun -np 8 python ./profile_halos.py --parallel
>>
>> When I run this with the current tip (ccfe34e70803) the total memory
>> usage grows to >24GB. With the last good changeset the total memory usage
>> never gets above ~8.5GB (estimated from top).
>>
>> It'd be great if we could find out what the problem is and fix it,
>> because this is a major performance regression for me, that, as I already
>> said, is seriously impacting my ability to do analysis with the current yt
>> tip. Let me know if I should file a BB issue about this, and/or if there's
>> some way I can assist with fixing this.
>>
>> Cheers,
>> Mike
>>
>> --
>> *********************************************************************
>> *                                                                   *
>> *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
>> *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
>> *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
>> *  skype username: mikekuhlen      Berkeley, CA 94720               *
>> *                                                                   *
>> *********************************************************************
>>
>
>
>
> --
> *********************************************************************
> *                                                                   *
> *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
> *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
> *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
> *  skype username: mikekuhlen      Berkeley, CA 94720               *
> *                                                                   *
> *********************************************************************
>
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