[yt-users] problem with merger tree

Luigi Iapichino LUIGI at uni-heidelberg.de
Tue Sep 17 02:12:43 PDT 2013


Hi Britton,

you are right, there was a comment (starting with # ) in the Enzo  
parameter file. The comment was on the line of   
MinimumOverDensityForRefinement . Enzo could run well with this  
comment, but yt complains about it (by the way, not only the merger  
tree, now I noticed that also a simple slice does not work). I removed  
the comment and the merger tree script is running. Thanks!

Cheers,

   Luigi

P.S.: while installing yt 2.5.5 I had some issues; I will report to  
the list, in a different email.

Quoting Britton Smith <brittonsmith at gmail.com>:

> Hi Luigi,
>
> It looks like there is a strange line in the parameter file of one of your
> datasets and yt is failing trying to parse it.  You should be able to
> reproduce this problem by doing pf = load(<filename>) for each of the
> datasets.  When you figure out which one it is, can you post it with
> yt_lodgeit.py and let us have a look?
>
> Britton
>
>
> On Fri, Sep 13, 2013 at 2:51 PM, Luigi Iapichino   
> <luigi at uni-heidelberg.de>wrote:
>
>> Dear all,
>>
>> I'm trying to analyse (with the latest yt 2.5.5) a whole dataset from a
>> cosmological simulation of mine, run with Enzo 2.1, and to extract the
>> merger
>> tree of the most massive halo in the box. I'm trying to run the script
>> presented at the bottom of:
>>
>> http://yt-project.org/doc/analysis_modules/merger_tree.html
>>
>> but I get the following output:
>>
>> yt : [INFO     ] 2013-09-13 15:46:28,359 Loading plugins
>> from /home/hpc/pr95he/lu79qey3/.yt/my_plugins.py
>> Traceback (most recent call last):
>>   File "./merger-tree.py", line 32, in <module>
>>     MergerTree(restart_files=files, database=my_database)
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py",
>> line 200, in __init__
>>     self._run_halo_finder_add_to_db()
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py",
>> line 246, in _run_halo_finder_add_to_db
>>     pf = load(file)
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/convenience.py",
>> line 77, in load
>>     return output_type_registry[candidates[0]](*args, **kwargs)
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/frontends/enzo/data_structures.py",
>> line 727, in __init__
>>     StaticOutput.__init__(self, filename, data_style,
>> file_style=file_style)
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/data_objects/static_output.py",
>> line 104, in __init__
>>     self._parse_parameter_file()
>>
>> File
>> "/home/hpc/pr95he/lu79qey3/remotefs/yt-2.5/src/yt-hg/yt/frontends/enzo/data_structures.py",
>> line 838, in _parse_parameter_file
>>     vals = np.array([pcast(i) for i in vals if i != "-99999"])
>> ValueError: could not convert string to float: #
>>
>>
>> I am pretty sure that the paths to the files and to the database to be
>> saved
>> are sensible.
>> Looking forward to your suggestions,
>> Cheers,
>>
>>   Luigi
>>
>> --
>>
>> ---------------------------------------------------------------
>>
>> Luigi Iapichino
>> Universität Heidelberg, Zentrum für Astronomie
>> Institut für Theoretische Astrophysik
>> Philosophenweg 12, D-69120 Heidelberg, Germany
>> Tel: +49 6221 548983, Fax: +49 6221 544221
>> e-mail: luigi at uni-heidelberg.de
>> URL: http://www.ita.uni-heidelberg.de/~luigi/
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>



-- 
Luigi Iapichino
Universität Heidelberg, Zentrum für Astronomie
Institut für Theoretische Astrophysik
Philosophenweg 12, D-69120 Heidelberg, Germany
Tel: +49 6221 548983, Fax: +49 6221 544221
e-mail: luigi at uni-heidelberg.de
URL: http://www.ita.uni-heidelberg.de/~luigi/




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