Mailman 3 April 2009 - yt-users

Halo finder changes
by Matthew Turk 13 May '09

13 May '09

Hi everyone, Stephen Skory has added the Friends-of-friends halo finder to the yt trunk (not yt-1.0) and we've now enabled it as a possibility for finding halos in a simulation. Because there are now two mechanisms for finding halos, we've also changed the API a little bit and made the halo finders available through yt.mods. So to run the HOP halo finder you would do the following: from yt.mods import * pf = load("data0001") halo_list = HaloFinder(pf) and to run FOF you have to call it slightly differently: from yt.mods import * pf = load("data0001") halo_list = FOFHaloFinder(pf) To get FOF to compile, you'll have to rerun "python setup.py develop" or "python setup.py install" depending on how yt was installed initially. (The install_script does the former, but most hand-installs do the latter.) With this new API, both halo finders run in parallel. I'll save any discussion of that for Stephen, however, as there are some caveats to running HOP in parallel. Additionally, as of right now they dont scale as well as we'd like -- but we're working on it. Additionally, as a result of this change we have intentionally broken compatibility by removing the import of the 'hop' module in yt/mods.py. Hopefully this has not caused too many problems; all of the old, largely duplicated-in-multiple-places classes and interfaces have now been consolidated and placed in yt/lagos/HaloFinding.py. Thanks to Stephen for his hard work adding in FOF and working with the parallel interface! Best wishes, and let us know if there are any problems, Matt

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Install, osx 10.4
by david collins 01 May '09

01 May '09

Hi-- I'm trying to put yt on my 10.4 power pc laptop (Methuselah). I did: svn export http://svn.enzotools.org/yt/trunk/doc/install_script.sh DEST_DIR=$HOME/local bash install_script.sh I then get the error below Any thoughts? Thanks, d. Installing into /Users/dcollins/local INST_WXPYTHON=0 Downloading HDF5 Downloading hdf5-1.6.8.tar.gz from yt.enzotools.org Downloading zlib-1.2.3.tar.bz2 from yt.enzotools.org Downloading Python-2.6.1.tgz from yt.enzotools.org Downloading numpy-1.2.1.tar.gz from yt.enzotools.org Downloading matplotlib-0.98.5.2.tar.gz from yt.enzotools.org Downloading ipython-0.9.1.tar.gz from yt.enzotools.org Downloading tables-2.1.tar.gz from yt.enzotools.org Setting YT_DIR=/Users/dcollins/local/src/yt-trunk-svn/ Installing setuptools Failure. Check /Users/dcollins/local/yt_install.log. %> cat /Users/dcollins/local/yt_install.log Traceback (most recent call last): File "/Users/dcollins/local/src/yt-trunk-svn//ez_setup.py", line 269, in <module> main(sys.argv[1:]) File "/Users/dcollins/local/src/yt-trunk-svn//ez_setup.py", line 201, in main egg = download_setuptools(version, delay=0) File "/Users/dcollins/local/src/yt-trunk-svn//ez_setup.py", line 123, in download_setuptools import urllib2, shutil File "/Users/dcollins/local//lib/python2.6/urllib2.py", line 92, in <module> import httplib File "/Users/dcollins/local//lib/python2.6/httplib.py", line 77, in <module> import mimetools File "/Users/dcollins/local//lib/python2.6/mimetools.py", line 6, in <module> import tempfile File "/Users/dcollins/local//lib/python2.6/tempfile.py", line 34, in <module> from random import Random as _Random File "/Users/dcollins/local//lib/python2.6/random.py", line 871, in <module> _inst = Random() File "/Users/dcollins/local//lib/python2.6/random.py", line 96, in __init__ self.seed(x) File "/Users/dcollins/local//lib/python2.6/random.py", line 115, in seed super(Random, self).seed(a) SystemError: error return without exception set

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Particle Callback Error in Parallel Projections
by Devin Silvia 14 Apr '09

14 Apr '09

Hi, I am currently running into an issue when I try to carry out parallel projections with particle overlay. Also long as I don't use too many processors things run just fine but the projections only have some of the particles. Here is an example of the commands in my script: plotx = pc.add_projection("Density", 0, weight_field="Dust") plotx.add_callback(ParticleCallback(0, 1.0, p_size=1.0, col='k')) ploty = pc.add_projection("Density", 1, weight_field="Dust") ploty.add_callback(ParticleCallback(1, 1.0, p_size=1.0, col='k')) plotz = pc.add_projection("Density", 2, weight_field="Dust") plotz.add_callback(ParticleCallback(2, 1.0, p_size=1.0, col='k')) In addition, if I use too many processors and the one of the processors doesn't have any particles, I get the following error: Particle bounding box: 0.0 1.0 0.0 1.0 1.5 2.5 Traceback (most recent call last): Particle px extrema File "longbox.py", line 13, in <module> pc.save("DD%4.4d/DD%4.4d" % (i,i)) File "/home/solo/student/brittons/local/x86_64/lib/python2.5/site-packages/yt/raven/PlotCollection.py", line 80, in save override=override)) File "/home/solo/student/brittons/local/x86_64/lib/python2.5/site-packages/yt/raven/PlotTypes.py", line 110, in save_image self._redraw_image() File "/home/solo/student/brittons/local/x86_64/lib/python2.5/site-packages/yt/raven/PlotTypes.py", line 312, in _redraw_image self._run_callbacks() File "/home/solo/student/brittons/local/x86_64/lib/python2.5/site-packages/yt/raven/PlotTypes.py", line 183, in _run_callbacks cb(self) File "/home/solo/student/brittons/local/x86_64/lib/python2.5/site-packages/yt/raven/Callbacks.py", line 177, in __call__ print "Particle px extrema", particles_x.min(), particles_x.max(), \ ValueError: zero-size array to ufunc.reduce without identity Any help with this would be appreciated. Thanks, Devin -- Devin W. Silvia Graduate Student/Research Assistant Center for Astrophysics and Space Astronomy University of Colorado at Boulder http://mdbworks.net/devin

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Display variable error?
by david collins 01 Apr '09

01 Apr '09

Hi, all-- Has anyone seen this error, and do you have a way to get around it without re-launching yt? <error> plt.clf() File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/pyplot.py", line 336, in clf gcf().clf() File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/pyplot.py", line 273, in gcf return figure() File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/pyplot.py", line 251, in figure **kwargs) File "/nics/b/home/collins/local_xt5/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager window = Tk.Tk() File "/nics/b/home/collins/local_xt5//lib/python2.6/lib-tk/Tkinter.py", line 1643, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable </error> I'm running yt on kraken xt5 through a screen session that I have re-started after logging out and logging back in. This has not happened on other machines I've done this one. I tried setenv DISPLAY 666.666.6.6:0 (with the ip of the beast replaced with something real) but it didn't work. Thanks, d.

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