Mailman 3 August 2013 - yt-dev

Issue #619: user-defined outputs with Athena (yt_analysis/yt)
by Anonymous 05 Aug '13

05 Aug '13

New issue 619: user-defined outputs with Athena https://bitbucket.org/yt_analysis/yt/issue/619/user-defined-outputs-with-at… Anonymous: Dear Developers, I would like to visualize/analyze some streaming-nstability simulation outputs created with Athena with yt. The output is a user-defined variable, such as the particle density enhancement. The (2-d) data is written to a .vtk file which I tried to read with yt using the load command. I Immediately get errors. Here is the session information: pf = load("id0/Streaming2d.0000.difdpar.vtk") yt : [INFO ] 2013-08-05 15:30:17,851 Temporarily setting domain_right_edge = -domain_left_edge. This will be corrected automatically if it is not the case. yt : [INFO ] 2013-08-05 15:30:17,855 Parameters: current_time = 0 yt : [INFO ] 2013-08-05 15:30:17,855 Parameters: domain_dimensions = [64 64 1] yt : [INFO ] 2013-08-05 15:30:17,856 Parameters: domain_left_edge = [-1. -1. 0.] yt : [INFO ] 2013-08-05 15:30:17,857 Parameters: domain_right_edge = [ 1. 1. -0.] yt : [INFO ] 2013-08-05 15:30:17,858 Parameters: cosmological_simulation = 0.0 yt : [WARNING ] 2013-08-05 15:30:17,860 Dimensionality less than 3: reverting to overlap_proj --------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-3-fa5200178679> in <module>() ----> 1 pf = load("id0/Streaming2d.0000.difdpar.vtk") /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/convenience.pyc in load(*args, **kwargs) 75 if c._is_valid(*args, **kwargs): candidates.append(n) 76 if len(candidates) == 1: ---> 77 return output_type_registry[candidates[0]](*args, **kwargs) 78 if len(candidates) == 0: 79 if ytcfg.get("yt", "enzo_db") != '' \ /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in __init__(self, filename, data_style, storage_filename, parameters) 353 # instantiated so that we can make sure we have the correct left 354 # and right domain edges. --> 355 self.h 356 357 def _set_units(self): /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/data_objects/static_output.pyc in hierarchy(self) 201 raise RuntimeError("You should not instantiate StaticOutput.") 202 self._instantiated_hierarchy = self._hierarchy_class( --> 203 self, data_style=self.data_style) 204 return self._instantiated_hierarchy 205 h = hierarchy # alias /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in __init__(self, pf, data_style) 129 #self.directory = os.path.dirname(self.hierarchy_filename) 130 self._fhandle = file(self.hierarchy_filename,'rb') --> 131 AMRHierarchy.__init__(self, pf, data_style) 132 133 self._fhandle.close() /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 70 71 mylog.debug("Parsing hierarchy.") ---> 72 self._parse_hierarchy() 73 74 mylog.debug("Constructing grid objects.") /home/hlcapelo/.local/lib/python2.7/site-packages/yt-2.6dev-py2.7-linux-x86_64.egg/yt/frontends/athena/data_structures.pyc in _parse_hierarchy(self) 251 line = f.readline() 252 f.close() --> 253 levels[j] = gridread['level'] 254 glis[j,0] = gridread['left_edge'][0] 255 glis[j,1] = gridread['left_edge'][1] KeyError: 'level'

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Issue #618: Install script fails when compiling with gcc provided by MESA sdk (yt_analysis/yt)
by Nathan Goldbaum 05 Aug '13

05 Aug '13

New issue 618: Install script fails when compiling with gcc provided by MESA sdk https://bitbucket.org/yt_analysis/yt/issue/618/install-script-fails-when-co… Nathan Goldbaum: It seems a lot of people have the gcc provided by the [MESA](http://mesa.sourceforge.net/) sdk in their `$PATH`. The install script currently fails while trying to compile mysql using this compiler. I've only seen this on a mac, and while building yt with xcode's gcc still works, it's a bit confusing for new users who aren't familiar with POSIX semantics. Fixing this will require testing with a MESA install on a mac. Hopefully there's some way to determine that we're using the MESA sdk compilers so we can either warn users or adjust the defaults automagically.

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Issue #617: Load single pf into Rockstar (yt_analysis/yt)
by Sam Skillman 05 Aug '13

05 Aug '13

New issue 617: Load single pf into Rockstar https://bitbucket.org/yt_analysis/yt/issue/617/load-single-pf-into-rockstar Sam Skillman: It would be nice to be able to do: ``` #!python rh = RockstarHaloFinder(pf) ``` where pf is a single dataset and not a TimeSeriesData. Responsible: samskillman

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Issue #616: Loading vtk files from Athena joined with their join_vtk.c executable (yt_analysis/yt)
by Anonymous 03 Aug '13

03 Aug '13

New issue 616: Loading vtk files from Athena joined with their join_vtk.c executable https://bitbucket.org/yt_analysis/yt/issue/616/loading-vtk-files-from-athen… Anonymous: It seems that when loading Athena vtk files, if the file was created by the Athena supplied executable join_vtk (for stitching together vtk files created from the different processors in an mpi run) then the loaded data is missing all the fields except the 'density' field.

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Away
by Matthew Turk 02 Aug '13

02 Aug '13

Hi all, Just a heads up, I will be away until the 15th or so. Don't feel that PRs need to wait for me to return unless they are something that definitely needs my attention. Matt

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Issue #615: plots look grainy and not so nice under matplotlib 1.3.0 (yt_analysis/yt)
by Nathan Goldbaum 02 Aug '13

02 Aug '13

New issue 615: plots look grainy and not so nice under matplotlib 1.3.0 https://bitbucket.org/yt_analysis/yt/issue/615/plots-look-grainy-and-not-so… Nathan Goldbaum: Something must have changed internally in matplotlib, as png plots are now significantly lower resolution by default. Responsible: ngoldbaum

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Issue #614: yt's libraries are not compatible with CentOS binaries (yt_analysis/yt)
by Nathan Goldbaum 31 Jul '13

31 Jul '13

New issue 614: yt's libraries are not compatible with CentOS binaries https://bitbucket.org/yt_analysis/yt/issue/614/yts-libraries-are-not-compat… Nathan Goldbaum: I was trying to use `eog` to look at some images on a supercomputer. Under the yt environment, I get a seg fault when I try to use `eog`, but after deactivating and trying again, everything works correctly. `eog` is dynamically loading yt's freetype and libz. I've pasted a shell session with information about this issue below: ``` #!bash [goldbaum@hyades ~]$ eog Segmentation fault [goldbaum@hyades ~]$ which eog /usr/bin/eog [goldbaum@hyades ~]$ ldd /usr/bin/eog | grep yt libfreetype.so.6 => /home/goldbaum/yt-x86_64/lib/libfreetype.so.6 (0x00002b9c0759f000) libz.so.1 => /home/goldbaum/yt-x86_64/lib/libz.so.1 (0x00002b9c0787b000) [goldbaum@hyades ~]$ deactivate [goldbaum@hyades ~]$ [goldbaum@hyades ~]$ eog [goldbaum@hyades ~]$ ldd /usr/bin/eog | grep 'freetype\|libz' libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00000037af800000) libz.so.1 => /lib64/libz.so.1 (0x00000037ab800000) [goldbaum@hyades ~]$ cat /etc/centos-release CentOS release 6.3 (Final) ``` It's not clear to me why yt's freetype and/or libz are incompatible with the CentOS libraries. @xarthisius, do you have any idea what's going on here? It's probably not worth spending too much time on this, but this issue can at least serve as a reference point. The workaround for this issue is just to deactivate the yt environment.

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