Mailman 3 April 2010 - yt-users

Terminal disappears while downloading
by robyn April 30, 2010

April 30, 2010

This has happened several times on 2 of my machines. Installing with the install_ script and it continues for 10-15 minutes, having downloaded the tars and starting to compile. Suddenly without any warning the terminal just vanishes. When I bring it back up and restart, installation resumes but vanishes again after a few seconds. Installation completed fine on my 3rd machine -- within minutes of the problem on the other 2. Network connections on my end are okay. One of the logs did say something about "failure to retreive" something just before the terminal vanished. -Thanks.

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Scripting with Quicktime Pro
by John Wise April 29, 2010

April 29, 2010

Hi all, This isn't yt related, but I thought most of you would benefit from this. I usually use Quicktime Pro (v7) to make movies. I got tired of manually opening up the images and saving them, so I found that Applescript can easily automate this. It's pretty straightforward, and you can make a shell or python script that writes the Applescript and executes it. Here's an example Applescript http://paste.enzotools.org/show/480/ To run it, type "osascript script_name.applescript". Here's an example Python routine that makes the script and runs it. http://paste.enzotools.org/show/481/ Unfortunately this doesn't work with the new QuickTime Player in Snow Leopard because they removed the image sequence loader for some reason. I had to reinstall the old QT from the Optional Installs in the install DVD. Cheers, John

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Halo Finding bugfix
by Stephen Skory April 28, 2010

April 28, 2010

Hi all, I've just committed in trunk r1705 a bugfix to HaloFinding.py that addresses a problem some users were seeing. In particular, the same data field was being repeatedly read off disk, once per halo, which seriously degraded performance. If you want to upgrade to the latest trunk version, "yt instinfo -u" should do it. _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Line through slice
by Nicholas Earl April 26, 2010

April 26, 2010

Hey community, Was wondering if anyone has any idea how I might put in a line at some x value when I do a Simple Slice. Just a simple line along the y-axis. Thanks for your time and effort, Nicholas Earl

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Error in build of kdtree
by Eric Hallman April 26, 2010

April 26, 2010

I am getting this error after Forthon install and make in the kdtree dir: login4% make Forthon -F gfortran --compile_first fKD_source --no2underscores --with- numpy --fopt "-O3" fKD fKD_source.f90 IN FORTHON_BUILDER Traceback (most recent call last): File "/work/01059/tg803229/raft-0.1a/local/bin/Forthon", line 2, in <module> import Forthon.Forthon_builder File "/work/01059/tg803229/raft-0.1a/local/lib/python2.6/site- packages/Forthon/Forthon_builder.py", line 142, in <module> twounderscores=twounderscores) File "/work/01059/tg803229/raft-0.1a/local/lib/python2.6/site- packages/Forthon/compilers.py", line 66, in __init__ if self.linux_pathscale() is not None: break File "/work/01059/tg803229/raft-0.1a/local/lib/python2.6/site- packages/Forthon/compilers.py", line 352, in linux_pathscale if usecompiler('pathscale','pathf95'): NameError: global name 'usecompiler' is not defined make: *** [fKD] Error 1 Any ideas would help. Thanks! Eric Hallman Google Voice: (774) 469-0278 hallman13(a)gmail.com

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libpng and new volume rendering methods
by Matthew Turk April 25, 2010

April 25, 2010

Hi everyone, (if you're on yt-1.6, feel free to ignore this message!) I've backported the multivariate volume rendering (for instance: http://yt.enzotools.org/attachment/wiki/Screenshots/hiiregion_rgb.png http://yt.enzotools.org/attachment/wiki/Screenshots/Reion512_600px.png http://yt.enzotools.org/attachment/wiki/Screenshots/SimB-BH.png ) to the yt trunk; this also comes with the ability to project through a simulation along a non-orthogonal vector, so you can create images that, for instance, peer down the L vector of a gas cloud but include contributions from all the intervening gas -- it's much faster and higher quality than stacking cutting planes, which was the old method for doing this. (Example: http://yt.enzotools.org/attachment/wiki/Screenshots/halo_0029.png ) The new backend for volume rendering should be API compatible with the old, but if you update your installation you will have to rebuild the C extensions either by doing: $ yt instinfo -u or by re-installing. The new multivariate volume rendering as well as the off-axis projecting have not yet been documented. This also comes with a direct PNG writer, which is much faster than using matplotlib for outputting raw images; it also comes with a couple colormaps. This requires that libpng be installed. yt will do its best to locate libpng, but if it cannot find it, you will have to supply it in png.cfg, much like for hdf5 -- however, the installation script has been updating to install libpng if requested, so if you run into any problems, rerun a new version of the installation script. (Running it over top of an old installation should be fine, as it will just conduct the necessary upgrades.) For the next release, both the new volume rendering mechanism and the image writer will be documented in detail; the release is probably about a week or two away. Let me know if you're eager to get your hands on the API docs for either of these things and I'll shoot you some sample scripts. If you run into any problems, let us know! Best, Matt

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'dx' field from ortho_ray
by Michael Kuhlen April 24, 2010

April 24, 2010

It seems that ortho_ray produces a 'dx' field (also 'CellLength') that is not the same order as the other data fields. This is again for a 1D simulation, this time with a few levels of AMR on. ray = pf.h.ortho_ray(0, [0.5, 0.5]) print ray['x'] yt INFO 2010-04-23 16:54:42,181 Getting field x from 6 [ 0.005 0.015 0.025 0.035 0.045 0.055 0.065 0.075 0.085 0.095 0.105 0.115 0.125 0.135 0.145 0.155 0.165 0.175 0.185 0.195 0.205 0.215 0.225 0.235 0.245 0.255 0.265 0.275 0.285 0.295 0.305 0.315 0.325 0.335 0.345 0.355 0.365 0.375 0.385 0.395 0.405 0.415 0.425 0.435 0.445 0.455 0.465 0.475 0.485 0.495 0.505 0.515 0.525 0.535 0.545 0.555 0.5625 0.5675 0.5725 0.5775 0.5825 0.5875 0.595 0.605 0.615 0.625 0.635 0.645 0.655 0.665 0.675 0.685 0.695 0.705 0.7125 0.7175 0.72125 0.72375 0.725625 0.726875 0.728125 0.7290625 0.7296875 0.7303125 0.7309375 0.7315625 0.7321875 0.7328125 0.7334375 0.7340625 0.7346875 0.7353125 0.7359375 0.736875 0.738125 0.739375 0.74125 0.74375 0.7475 0.7525 0.7575 0.765 0.775 0.785 0.795 0.805 0.815 0.825 0.835 0.845 0.855 0.865 0.875 0.885 0.895 0.905 0.915 0.925 0.935 0.945 0.955 0.965 0.975 0.985 0.995 ] print ray['dx'] yt INFO 2010-04-23 16:54:42,232 Getting field dx from 6 [ 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.0025 0.0025 0.0025 0.0025 0.00125 0.00125 0.00125 0.00125 0.00125 0.00125 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625 0.000625] Any ideas how to fix this bug? Or some other way to access the ray's 'dx' values in the correct order? I suppose I could simply calculate the dx's myself from the 'x' field... Thanks, Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 601 Campbell Hall * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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Volume rendering - filenames
by Mike Butler April 22, 2010

April 22, 2010

Hello, This is probably a simple thing to fix, but I've been trying to use the volume rendering package on my data and am running into an error. If I follow the steps at http://paste.enzotools.org/show/404/ when I get to mi,ma = dd.quantities["Extrema"]("Density")[0] I get the error message at the bottom of this email. It seems that it is looking for files ending in .cpu000# rather than .grid.cpu000# like the default enzo output. I've tried doing a rename but then I get the same error but the other way around. Making a copy of the file with each filename works if I'm just doing a single image, but I'm trying to make a movie so doing that for 100 files for 8 cpus each would be a bit tedious. If anyone knows a way around this or I'm doing something wrong, I'd appreciate any suggestions. Thanks -Mike In [8]: mi,ma=dd.quantities["Extrema"]("Density")[0] ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (105, 0)) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (72, 0)) ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (119, 0)) --------------------------------------------------------------------------- ReadingError Traceback (most recent call last) /home/butler85/yt/src/yt-trunk-svn/scripts/iyt in <module>() ----> 1 2 3 4 5 /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc in __call__(self, *args, **kwargs) 70 self._data_source.pf.h.io) 71 if lazy_reader and not self.force_unlazy: ---> 72 return self._call_func_lazy(args, kwargs) 73 else: 74 return self._call_func_unlazy(args, kwargs) /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc in _call_func_lazy(self, args, kwargs) 77 self.retvals = [ [] for i in range(self.n_ret)] 78 for gi,g in enumerate(self._get_grids()): ---> 79 rv = self.func(GridChildMaskWrapper(g, self._data_source), *args, **kwargs) 80 for i in range(self.n_ret): self.retvals[i].append(rv[i]) 81 g.clear_data() /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc in _Extrema(data, fields, filter) 385 mins, maxs = [], [] 386 for field in fields: --> 387 if data[field].size < 1: 388 mins.append(1e90) 389 maxs.append(-1e90) /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DerivedQuantities.pyc in __getitem__(self, item) 41 return getattr(self.grid, attr) 42 def __getitem__(self, item): ---> 43 return self.data_source._get_data_from_grid(self.grid, item) 44 45 class DerivedQuantity(ParallelAnalysisInterface): /home/butler85/yt/src/yt-trunk-svn/yt/lagos/BaseDataTypes.pyc in save_state(self, grid, field) 41 old_keys = grid.data.keys() 42 grid.field_parameters = self.field_parameters ---> 43 tr = func(self, grid, field) 44 grid.field_parameters = old_params 45 grid.data = dict( [(k, grid.data[k]) for k in old_keys] ) /home/butler85/yt/src/yt-trunk-svn/yt/lagos/BaseDataTypes.pyc in _get_data_from_grid(self, grid, field) 1660 else: 1661 pointI = self._get_point_indices(grid) -> 1662 if grid[field].size == 1: # dx, dy, dz, cellvolume 1663 t = grid[field] * na.ones(grid.ActiveDimensions, dtype='float64') 1664 return t[pointI].ravel() /home/butler85/yt/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in __getitem__(self, key) 133 """ 134 if not self.data.has_key(key): --> 135 self.get_data(key) 136 return self.data[key] 137 /home/butler85/yt/src/yt-trunk-svn/yt/lagos/BaseGridType.pyc in get_data(self, field) 166 return self.data[field] 167 try: --> 168 temp = self.hierarchy.io.pop(self, field) 169 self[field] = na.multiply(temp, conv_factor, temp) 170 except self.hierarchy.io._read_exception, exc: /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DataReadingFuncs.pyc in pop(self, grid, field) 55 else: 56 # We only read the one set and do not store it if it isn't pre-loaded ---> 57 return self._read_data_set(grid, field) 58 59 def peek(self, grid, field): /home/butler85/yt/src/yt-trunk-svn/yt/lagos/DataReadingFuncs.pyc in _read_data_set(self, grid, field) 232 def _read_data_set(self, grid, field): 233 return HDF5LightReader.ReadData(grid.filename, --> 234 "/Grid%08i/%s" % (grid.id, field)).swapaxes(0,2) 235 236 def _read_data_slice(self, grid, field, axis, coord): ReadingError: ReadHDF5DataSet: /home/butler85/sim/starsfuvamrrec/Cloud_128AMR4StarsFUV_0101.cpu0000 does not exist, or no read permissions

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bug in ortho_ray and derived fields?
by Michael Kuhlen April 21, 2010

April 21, 2010

Hi I'm experiencing some weird behavior with ortho_ray() when used with derived fields. I suspect this is a bug, but I'm new to yt, so maybe I'm doing something incorrectly. This is for a 1D Enzo simulation, and the only fields in the simulation dataset are Density, x-velocity, and TotalEnergy. I defined two derived fields, InternalEnergy and Pressure: ### define InternalEnergy field def _InternalEnergy(field, data): return data['TotalEnergy'] - 0.5*data['x-velocity']*data['x-velocity'] add_field('InternalEnergy', function=_InternalEnergy, units=r'\rm{erg}/\rm{g}') ### define Pressure field def _Pressure(field, data): return (data.pf['Gamma'] - 1.0) * data['Density'] * data['InternalEnergy'] add_field('Pressure', function=_Pressure, units=r'\rm{dyne}/\rm{cm}^{2}') Next I want to extract a ray of Density, x-velocity, Pressure, and InternalEnergy along the only dimension. I figured ortho_ray is the right tool. ray = pf.h.ortho_ray(0, [0.5, 0.5], ['x-velocity', 'Density', 'InternalEnergy', 'Pressure']) print ray.keys() This produces: ['Pressure', 'x', 'x-velocity', 'InternalEnergy', 'Density'] Perfect, everything as desired. However, if I change the order of the input fields, some disappear from the ray. Examples: (1) ray = pf.h.ortho_ray(0, [0.5, 0.5], ['Density', 'x-velocity', 'Pressure', 'InternalEnergy']) print ray.keys() ['x', 'x-velocity', 'Pressure', 'Density'] -- 'InternalEnergy' is missing. (2) ray = pf.h.ortho_ray(0, [0.5, 0.5], ['Pressure', 'Density', 'x-velocity']) print ray.keys() ['Pressure'] -- 'Density' and 'x-velocity' are missing. (3) ray = pf.h.ortho_ray(0, [0.5, 0.5], ['InternalEnergy', 'Density', 'x-velocity']) print ray.keys() ['InternalEnergy', 'Density'] -- 'x-velocity' is missing. The pattern I'm seeing here is that whenever 'InternalEnergy' is specified as an input only one field after it makes it into the ray. When 'Pressure' is specified, no further fields make it. I don't imagine this behavior is intended, but maybe it's due to some user error on my part? Thanks in advance for any clarifications. Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 601 Campbell Hall * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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Problem with yt and h5py
by Brian O'Shea April 18, 2010

April 18, 2010

Dear yt-users, I'm having a strange problem with yt (svn trunk, r1693). If I run this script: from yt.mods import * fn = "DD0050/DD0050" pf = load(fn) dd = pf.h.all_data() I get the following error: yt INFO 2010-04-18 13:41:48,183 Getting the binary hierarchy Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/OutputTypes.py", line 150, in _get_hierarchy self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) File "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line 374, in __init__ AMRHierarchy.__init__(self, pf, data_style) File "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line 55, in __init__ self._parse_hierarchy() File "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line 435, in _parse_hierarchy if self._parse_binary_hierarchy(): return File "/mnt/home/oshea/yt-x86_64/src/yt-trunk-svn/yt/lagos/HierarchyType.py", line 506, in _parse_binary_hierarchy self.grid_dimensions[:] = f["/ActiveDimensions"][:] File "/mnt/home/oshea/yt-x86_64/lib/python2.6/site-packages/h5py-1.2.0-py2.6-linux-x86_64.egg/h5py/highlevel.py", line 961, in __getitem__ basetype = self.id.dtype File "h5d.pyx", line 109, in h5py.h5d.DatasetID.dtype.__get__ (h5py/h5d.c:1423) File "h5t.pyx", line 364, in h5py.h5t.TypeID.dtype.__get__ (h5py/h5t.c:2919) File "h5t.pyx", line 367, in h5py.h5t.TypeID.py_dtype (h5py/h5t.c:2976) TypeError: No NumPy equivalent for TypeIntegerID exists I installed this version of yt on MSU's supercomputer using the install script at http://svn.enzotools.org/yt/trunk/doc/install_script.sh (the supercomputer uses gcc v4.1.2), and as far as I can tell everything relevant, including hdf5 and h5py, installed successfully. The same simple set of commands works fine on my laptop with the same dataset. I'm pointing my LD_LIBRARY_PATH environmental variable to the correct directory, so I don't think it's that. Any ideas about what's going on here? Some more system details: The output of uname -a for this system is is "Linux dev-amd09 2.6.16.60-0.21-smp #1 SMP Tue May 6 12:41:02 UTC 2008 x86_64 x86_64 x86_64 GNU/Linux". The system uses gcc v4.1.2 and I'm installing yt _without_ wxPython. Thanks, Brian

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