problem with merger tree
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@uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/
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
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@uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/ _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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
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
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@uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/ _______________________________________________ yt-users mailing list yt-users@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@uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/
participants (3)
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Britton Smith
-
Luigi Iapichino
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Luigi Iapichino