Mailman 3 June 2010 - yt-users

Slice issues
by Brian Crosby 08 Jul '10

08 Jul '10

Hi all, I've been trying to make a series of plots from the data dumps of an Enzo simulation, but am encountering problems when yt attempts to make slices. At first I thought it was due to some error in the recursion, but after making a much more direct script, it appears to come up as soon as slices are to be created. For what it's worth, projections are made without any problem, it's the slices that are giving me trouble. The output file is attached. Thanks, Brian

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New yt installation problem
by Dr. ABHIJIT BHATTACHARYYA 30 Jun '10

30 Jun '10

Hi After failure with the canonical install script I foloowed instruction for the manual installation procedure. This method gave me success. However, invoking the "iyt" gives me following warning (seems not a clean run). The good news is that ignoring this warning, I could plot Enzo data using pylab.plot. Here one important point I noticed is that, in earlier version, I had to use pylab.show() command to plot on the screen after declaration of pylab.xlabel, pylab.ylabel and pylab.plot commands. Here, as soon as I use pylab.xlabel, I find graphics window on the screen which adpts all the subsequient command and hence do not require any pylab.show(). For the warning, I checked all path is given in .cshrc. In ~/.ipython/ipy_user_conf.py file, the problem is given by "o = ip.options" line. Any handle? regs Abhijit > iyt Your PyGtk has set_interactive(), so you can use the more stable single-threaded Gtk mode. See https://bugs.launchpad.net/ipython/+bug/270856 --------------------------------------------------------------------------- IndentationError Traceback (most recent call last) /usr/local/lib/python2.6/site-packages/IPython/ipmaker.pyc in force_import(modname, force_reload) 61 reload(sys.modules[modname]) 62 else: ---> 63 __import__(modname) 64 65 IndentationError: unindent does not match any outer indentation level (ipy_user_conf.py, line 52) WARNING: Loading of ipy_user_conf failed. Welcome to yt! In [1]:

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Re: [yt-users] Iteration Problems
by Stephen Skory 29 Jun '10

29 Jun '10

Brian, >Traceback (most recent call last): > File "s_p_halos.py", line 46, in <module> > pc.save("test_images/%s_%i" % (pf,height)) > File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.5/yt/raven/PlotCollection.py", line 81, in save > override=override, force_save=force_save)) > File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.5/yt/raven/PlotTypes.py", line 112, in save_image > self._redraw_image() > File "/share/home/01450/bcrosby/yt-x86_64/src/yt-1.5/yt/raven/PlotTypes.py", line 352, in _redraw_image > newmin = na.nanmin(buff[bI]) >MemoryError >TACC: Cleaning up after job: 1440927 >TACC: Done. > > >So it would seem that I'm running up against a memory problem, but what we're hitting beyond that, I'm stumped. I think you might be running into a known & fixed memory leak in the halo finding stuff. It is fixed in the svn trunk version of yt, and you might consider switching to that. There will be a point release of yt very soon (today or in a few days) if you want to wait for that. There are a whole slew of changes between 1.5 and what's coming, which will be outlined in the announcement email. If you feel up to switching now, you can do that inside the yt-1.5 directory like this: svn sw http://svn.enzotools.org/yt/trunk python setup.py develop There are other possibilities, but this is the best one I can think of right now. Good luck! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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New yt installation problem
by Dr. ABHIJIT BHATTACHARYYA 28 Jun '10

28 Jun '10

Hi! I tried to install New yt version which shows the error due to following reason: ImportError: No module named binascii Please enlighten me to resolve the issue. Best Abhijit

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yt version 1.7 Release Announcement
by Britton Smith 28 Jun '10

28 Jun '10

We're proud to announce the release of yt version 1.7, an analysis and visualization toolkit for Adaptive Mesh Refinement data. (Just in time for the Enzo Workshop!) This release fixes a number of bugs, as well as numerous improvements to the code base and the documentation. Most prominently, it features "two-point functions" such as structure and correlation functions, a re-engineered volume rendering interface, multivariate volume rendering, off-axis projections, and a mechanism for complex postscript plot layout. Additionally, a major aspect of the drive to 1.7 has been re-engineering the API documentation to be better suited to interactive help (the "help(...)" call in python) as well as the documentation website ( http://yt.enzotools.org/doc/ ). Some of the changes since yt-1.6 (Released on January 22, 2010) include: * Direct writing of PNGs * Multi-band image writing * Parallel halo merger tree * Parallel structure function generator * Image pan and zoom object and display widget * Parallel volume rendering * Multivariate volume rendering, allowing for multiple forms of emission and absorption * Added Camera interface to volume rendering * Off-axis projection * Stereo (toe-in) volume rendering * DualEPS extension for better EPS construction * Rewritten, memory conservative and speed-improved contour finding algorithm * Speed improvements to volume rendering * Preliminary support for the Tiger code * Lightweight projection loading with projload * Improvements to yt.data_objects.time_series * Improvements to yt.extensions.EnzoSimulation * Speed improvements to basic HOP * Better docstrings and documentation (The full changelog: http://yt.enzotools.org/doc/changelog.html ) yt features native support for Enzo (http://lca.ucsd.edu/projects/enzo) data, providing a natural and intuitive way to address physical regions in space as well as processed data. Installation instructions can be found here: http://yt.enzotools.org/doc/installation.html . If you are running an older version of yt, re-obtaining and re-running the installation script should happily upgrade your installation. yt is a Free and Open Source project, and we invite you to get involved. For more information, join the yt-dev mailing list, or see the hacking guidelines on the Wiki: http://yt.enzotools.org/wiki/HackingGuidelines . We anticipate a few more releases in the 1.7 series as documentation and docstring coverage progress. Sincerely, The yt development team: Matthew Turk Stephen Skory Britton Smith John Wise Jeff Oishi Sam Skillman Devin Silvia David Collins

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Iteration Problems
by Brian Crosby 26 Jun '10

26 Jun '10

Hi all, I'm trying to run a script on Ranger that will go through a series of Enzo dump files (ie: RD0000/RedshiftOutput0000), find the halos, and make a series of slices and projections. The script works like a charm on a smaller data set running on the head node, but when I submit it as a batch job it goes through the first iteration and then exits without progressing to subsequent dumps. Does anyone have a clue why this would be happening? The only thing that I can come up with is that I'm trying to run the batch job in parallel, but the test on the head node was not. The script is attached. Thanks, Brian

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precision of TotalQuantity
by gso＠physics.ucsd.edu 19 Jun '10

19 Jun '10

My script below gives the max min and mean of a field, however, the mean seems to be only giving me 6 digits of accuracy as seen in the output: min 5.3512599744055807e-30 max 2.4254363112272260e-26 mean 7.9708800000000001e-29 it's very unlikely that the mean value has all those zeroes in it, is there a quick way to get higher accuracy using something similar to dd.quantites[] or do I have to calculate the total by looping over all the cells to get the higher precision I needed? From G.S. from yt.mods import * pf = EnzoStaticOutput("DD0273/DD0273") res=64 #v,c = pf.h.find_min("Density") #print v,c dd = pf.h.all_data() field = "Density" extreme = dd.quantities["Extrema"](field)[0] zmin = extreme[0] zmax = extreme[1] mean = dd.quantities["TotalQuantity"](field)[0]/res**3 print ("min %16.16e" % zmin) print ("max %16.16e" % zmax) print ("mean %16.16e" % mean)

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YT on new Snow Leopard install
by Nicholas Earl 16 Jun '10

16 Jun '10

Hey everyone, I'm having issues using yt on a fresh install of snow leopard. The 10.6 yt installation went perfect, but when I go to run a simple slice script, I'm getting this error: yt INFO 2010-06-15 20:16:15,452 Created plot collection with default plot-center = [1.0, 0.5, 0.0] Traceback (most recent call last): File "slices2D.py", line 9, in <module> p = pc.add_slice("Temperature",axis) File "/Users/earln/yt-i386/src/yt-trunk-svn/yt/raven/plot_collection.py", line 372, in add_slice size=fig_size, periodic=periodic)) File "/Users/earln/yt-i386/src/yt-trunk-svn/yt/raven/PlotTypes.py", line 314, in __init__ self.__init_temp_image(use_colorbar) File "/Users/earln/yt-i386/src/yt-trunk-svn/yt/raven/PlotTypes.py", line 347, in __init_temp_image shrink=0.95) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/figure.py", line 1045, in colorbar cb = cbar.Colorbar(cax, mappable, **kw) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/colorbar.py", line 647, in __init__ ColorbarBase.__init__(self, ax, **kw) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/colorbar.py", line 238, in __init__ self.draw_all() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/colorbar.py", line 249, in draw_all self._config_axes(X, Y) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/colorbar.py", line 276, in _config_axes ticks, ticklabels, offset_string = self._ticker() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/colorbar.py", line 415, in _ticker b = np.array(locator()) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/matplotlib/ticker.py", line 1069, in __call__ vmin = self.axis.get_minpos() AttributeError: DummyAxis instance has no attribute 'get_minpos' It seemed to me an issue with matplotlib, but I've tried many things including installing matplotlib from source separate from the yt installation, and it still fails. Any ideas? Thanks for your time and effort! Nicholas Earl

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fields in ghost zones
by Jean-Claude Passy 16 Jun '10

16 Jun '10

Dear all, in order to set up my simulation, I need to access the values of certain fields in the ghost zones. If I do something like: pf = load(data) region = pf.h.region(...) x = region[field] x contains the values of field for the physical grid only. Is there a way I can get the same 1D-array but with the ghost zones included as well ? Thanks for your help, Jean-Claude

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writing x-,y- and z positions in one file
by Agarwal, Shankar 10 Jun '10

10 Jun '10

Hi, I am trying to dump the particle_positions to a file. Here is my extremely inefficient script... from yt.mods import * import pickle fn = "RedshiftOutput0000" # parameter file to load pf = load(fn) # load data all_data = pf.h.all_data() particle_positions_x = all_data['particle_position_x'] particle_positions_y = all_data['particle_position_y'] particle_positions_z = all_data['particle_position_z'] Dark_Matter_Density = all_data['Dark_Matter_Density'] # this is a Dataset {32, 32, 64} f1 = open('junk1', 'w') f2 = open('junk2', 'w') f3 = open('junk3', 'w') s1 = str(particle_positions_x) s2 = str(particle_positions_y) s3 = str(particle_positions_z) f1.write(s1) f2.write(s2) f3.write(s3) f1.close() f2.close() f3.close() How can I write out x-,y- and z positions in three columns in the same file ? And how to handle the array Dark_Matter_Density ? Shankar KU Cosmology

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