[yt-users] No "NumberOfParticles" attribute for "YTRegion"

Sun Nov 17 10:36:43 PST 2013

Hi Nathan,

Thanks for sending that along.  I actually managed to get yt-3.0 and
rockstar to build using basically the same steps once I realized I
needed to be on the "tip" of rockstar.  Overall, having that step by
step process should be super useful for future users.

I also tried to run a test of the halo finder, but ran into the same
issue of having multi-mass particles.  I'm fiddling a bit with things
now to see if I can figure anything out on that front.

In working through this, I've starting wondering if it would be useful
to have some sort of hangout for people who either are interested in
using yt and rockstar so that we can work through what it takes to
make that happen, or people interested in trying to hammered out what
needs to be done to make the whole set up work a bit better for the
general user.

If there is interest in this, we could look into finding a time that works.

-Devin

On Sun, Nov 17, 2013 at 1:37 AM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> Ok, with Matt's suggestion I was able to get this working.
>
> How to get Rockstar working with yt-3.0:
>
> 1. Clone Matt's fork of Rockstar (http://bitbucket.org/matthewturk/rockstar)
> 2. Update to the tip (hg up 5223577)
> 3. Build rockstar as a library (make lib)
> 4. Put the resulting library (librockstar.so) in a location where it will be
> found during dynamic linking (e.g. LD_LIBRARY_PATH or /usr/local/lib)
> 5. Navigate to the yt-3.0 repository.  Echo the path to the library into a
> text file name rockstar.cfg (echo /usr/local/lib > rockstar.cfg).
> 6. Do 'python setup.py develop' yt should build the rockstar interface and
> link against librockstar.
> 7. Run your script.  Note that your script must be run in parallel.
>
> Unfortunately I wasn't able to actually *run* rockstar since I don't have
> any DM datasets with only single particle mass.  I think I have some
> DM+stars datasets that will work but I'm not sure how to pass a filtered
> particle type to the halo finder.  Matt, do you happen to know how to set
> that up?
>
> Hope that's helpful for others who have issues with rockstar setting up.
> Note or the future that the specific changeset I reference in step 2 will
> probably not be correct for very long since I think Matt wants to rearrange
> things so that fresh clones of the repo will be created with a working
> changeset.
>
> -Nathan
>
>
> On Sat, Nov 16, 2013 at 8:24 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>
>> Hi Nathan,
>>
>> My rock star repo has a default branch which is not the one that works;
>> the tip should, however. I'll address that as soon as I can.
>>
>> Matt
>>
>> On Nov 16, 2013 9:11 PM, "Nathan Goldbaum" <nathan12343 at gmail.com> wrote:
>>>
>>> I take that back, I just tried to compile yt’s rockstar interface,
>>> linking against a fresh clone of Matt’s Rockstar repo and got the same gcc
>>> error as Devin:
>>>
>>> http://paste.yt-project.org/show/4065/
>>>
>>> On November 16, 2013 at 5:27:57 PM, Nathan Goldbaum
>>> (nathan12343 at gmail.com) wrote:
>>>
>>> Hi Devin,
>>>
>>> This is a shot in the dark, but it might be that you have old
>>> autogenerated C files that are getting compiled.  I think if the setup.py
>>> script for the rockstar interface is written properly, this shouldn't be a
>>> problem - perhaps there is a bug there.
>>>
>>> Can you remove all of the .c and .so files in the yt installation and try
>>> rebuilding again?
>>>
>>> find . -name '*.so' | xargs rm
>>> find . -name '*.c' | xargs rm
>>>
>>> -Nathan
>>>
>>>
>>> On Sat, Nov 16, 2013 at 5:06 PM, Devin Silvia <devin.silvia at gmail.com>
>>> wrote:
>>>>
>>>> Hi Matt,
>>>>
>>>> I discovered that I was on an outdated yt-3.0 repo (got confused
>>>> jumping between machines).  However, after updating my yt-3.0 repo, I
>>>> can't seem to get yt-3.0 to build with rockstar.  I've downloaded the
>>>> rockstar bitbucket repo and put the directory into rockstar.cfg.  When
>>>> I try to do "python setup.py build_ext -i -f" I get the following
>>>> error when it get to building rockstar:
>>>>
>>>> http://paste.yt-project.org/show/4064/
>>>>
>>>> Most of it seems to be warnings, but the errors look like something
>>>> that I'm hoping someone more familiar with the code might be able to
>>>> parse.
>>>>
>>>> Thanks,
>>>> Devin
>>>>
>>>>
>>>> On Fri, Nov 15, 2013 at 6:18 PM, Matthew Turk <matthewturk at gmail.com>
>>>> wrote:
>>>> > Hi Devin,
>>>> >
>>>> > Your traceback doesn't match my rockstar.py file -- which hash are you
>>>> > on?
>>>> >
>>>> > -Matt
>>>> >
>>>> > On Fri, Nov 15, 2013 at 5:48 PM, Devin Silvia <devin.silvia at gmail.com>
>>>> > wrote:
>>>> >> Hi all,
>>>> >>
>>>> >> I've been trying to get yt-3.0 and the rockstar halofinder to work
>>>> >> and
>>>> >> I'm at the point where I *think* that my yt-3.0 install and rockstar
>>>> >> are happily talking to each other, but when it goes to actually run
>>>> >> the halofinder on my dataset, I get this issue:
>>>> >>
>>>> >> http://paste.yt-project.org/show/4060/
>>>> >>
>>>> >> It seems like something isn't being done right in terms of accessing
>>>> >> the particle information in the dataset, but I can't digest enough of
>>>> >> the yt source to understand why this is the case.  If anyone has any
>>>> >> thoughts as to what is going wrong, I'd appreciate it.
>>>> >>
>>>> >> For what it's worth, this is the simple script I am using:
>>>> >>
>>>> >> http://paste.yt-project.org/show/4062/
>>>> >>
>>>> >> Thanks!
>>>> >> Devin
>>>> >>
>>>> >> --
>>>> >> Devin W. Silvia
>>>> >> Research Associate
>>>> >> Department of Physics and Astronomy
>>>> >> Michigan State University
>>>> >> www.devinsilvia.com
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>>>>
>>>>
>>>>
>>>> --
>>>> Devin W. Silvia
>>>> Research Associate
>>>> Department of Physics and Astronomy
>>>> Michigan State University
>>>> www.devinsilvia.com
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-- 
Devin W. Silvia
Research Associate
Department of Physics and Astronomy
Michigan State University
www.devinsilvia.com