Mailman 3 March 2010 - yt-users

Call for testing: VTK on Snow Leopard
by Matthew Turk 16 Mar '10

16 Mar '10

Hi all, I've constructed some packages of VTK on Snow Leopard. If you've used the Snow Leopard installation script ("install_script_osx106.sh") to install yt and Python on your machine, I believe they should work -- and I'd love to hear if they do or don't, as we'd really like to start moving the GUI over to the VTK/Matplotlib/Traits GUI that we've been working on for about a year. This will enable a lot better interaction between you and your data, and we're going to be able to drop in support for things like OpenCL, OpenGL, and the volume renderer right inside that framework. (An older, development screenshot of the new GUI: http://yt.enzotools.org/attachment/wiki/Screenshots/reason_v2.png -- but things have improved since then!) The process has been described on a Wiki page: http://yt.enzotools.org/wiki/VTKOnSnowLeopard so if you are interested, give it a go and let me know how it works for you. Best, Matt

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file permissions
by Stephen Skory 16 Mar '10

16 Mar '10

Hi all, I'm attempting to load an enzo dataset in a directory I don't have write permissions for. I am getting an error I believe because it's trying to write the binary hierarchy, but it can't. I am running Python in a directory I can write to, so can I either have yt write in the CWD or just skip the binary hierarchy? Thanks! >>> pf = load("/lustre/scratch/darkness/X2560/Dumps/RD0020/RD0020") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/convenience.py", line 77, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/lagos/OutputTypes.py", line 59, in __new__ _pf_store.check_pf(obj) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 152, in check_pf self.insert_pf(pf) File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 166, in insert_pf self.flush_db() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 182, in flush_db self._write_out() File "/lustre/scratch/proj/yt_common/trunk/lib/python2.6/site-packages/yt-2.0dev-py2.6-linux-x86_64.egg/yt/fido/ParameterFileStorage.py", line 196, in _write_out f.close() IOError: [Errno 122] Disk quota exceeded _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

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Analyzing DM-only run
by kcai＠pa.uky.edu 12 Mar '10

12 Mar '10

Hi Matt and Britton, Thank you both for teaching me how to plot particles in the past. Now that I got rid of the redundant particles in the initial conditions, it is desirable to look at the subsequent evolution in more detail - in particular, the sphere of particles still got destroyed fairly quickly. So we suspect it is the initial velocity field that was not set up properly. However, I tried to use p = pc.add_slice('particle_density_pyx', 0) p.modify["velocity"]() but failed (the add_slice part works): Traceback (most recent call last): File "DM_plots.py", line 14, in <module> pc.save("RD0000/Redshift199") File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotCollection.py", line 81, in save override=override, force_save=force_save)) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 112, in save_image self._redraw_image() File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 374, in _redraw_image self._run_callbacks() File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 238, in _run_callbacks cb(self) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 75, in __call__ return qcb(plot) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 102, in __call__ plot.data[self.field_x] - self.bv_x, File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in __getitem__ self.get_data(key) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 584, in get_data if self._generate_field(field): File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 606, in _generate_field self.pf.field_info[field].check_available(self) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 267, in check_available validator(data) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 365, in __call__ raise NeedsDataField(doesnt_have) yt.lagos.FieldInfoContainer.NeedsDataField: (['y-velocity']) >>> pc.save("RD0000/Redshift199") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotCollection.py", line 81, in save override=override, force_save=force_save)) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 112, in save_image self._redraw_image() File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 374, in _redraw_image self._run_callbacks() File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/PlotTypes.py", line 238, in _run_callbacks cb(self) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 75, in __call__ return qcb(plot) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/raven/Callbacks.py", line 102, in __call__ plot.data[self.field_x] - self.bv_x, File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in __getitem__ self.get_data(key) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 584, in get_data if self._generate_field(field): File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 606, in _generate_field self.pf.field_info[field].check_available(self) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 267, in check_available validator(data) File "/share/home/kca223/lib/python2.6/site-packages/yt-1.6-py2.6-linux-x86_64.egg/yt/lagos/FieldInfoContainer.py", line 365, in __call__ raise NeedsDataField(doesnt_have) yt.lagos.FieldInfoContainer.NeedsDataField: (['y-velocity']) and I tried pc.add_slice('ParticleVelocityMagnitude', 0) and got segfault. Do you have any suggestions? In addition, how may I smooth the particle density and see more structures? Thanks a lot, Kai Quoting Matthew Turk <matthewturk(a)gmail.com>: > Hi Kai, > > You're right, good luck. > > -MAtt > > On Thu, Mar 11, 2010 at 10:42 PM, <kcai(a)pa.uky.edu> wrote: >> Hi Matt, >> Sorry for responding a bit late - I was out for dinner. We got a visitor >> here... >> >> I did find the gdb command you sent me a while ago, but looks like I get >> the problem fixed already - I found I can not only reset the >> NumberOfParticles, >> but also the "size" of the ParticleField[] array. So I set it to be the same >> as NumberOfParticles. Now: not only I get a perfect sphere of particles with >> nothing outside initially; and no segfaults with the YT script now. So you >> are right - it's those redundant array elements which caused the trouble. >> So it may not be necessary to get a "backtrace" now - don't you think? >> >> Thanks, >> Kai >> >> Quoting Matthew Turk <matthewturk(a)gmail.com>: >> >>> Use gdb, get a backtrace. Alternately, get a core dump and a >>> backtrace off that. If it's really segfaulting, the problem needs to >>> be debugged that way. >>> >>> On Thu, Mar 11, 2010 at 6:00 PM, <kcai(a)pa.uky.edu> wrote: >>>> >>>> Hi Matt, >>>> Thanks for helping out. Here is what I got (I don't know what is a "gdb >>>> backtrace"): >>>> >>>>> python2.6 -i DM_plots.py >>>> >>>> /home/kca223/lib/python2.6/site-packages/IPython/Magic.py:38: >>>> DeprecationWarning: the sets module is deprecated >>>> from sets import Set >>>> yt INFO 2010-03-11 18:34:20,059 Created plot collection >>>> with >>>> default plot-center = [0.5, 0.5, 0.5] >>>> yt INFO 2010-03-11 18:34:20,172 Getting the binary >>>> hierarchy >>>> yt INFO 2010-03-11 18:34:20,174 Finished with binary >>>> hierarchy >>>> reading >>>> yt INFO 2010-03-11 18:34:20,285 Getting field >>>> particle_position_y from 1 >>>> yt INFO 2010-03-11 18:34:20,285 Getting particle_position_y >>>> using ParticleIO >>>> yt INFO 2010-03-11 18:34:20,597 Getting field >>>> particle_position_z from 1 >>>> yt INFO 2010-03-11 18:34:20,597 Getting particle_position_z >>>> using ParticleIO >>>> yt INFO 2010-03-11 18:34:21,214 Generating overlap masks >>>> for >>>> level 0 >>>> Reading and masking grids 100% >>>> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: >>>> 00:00:00 >>>> yt INFO 2010-03-11 18:34:21,215 Finished calculating >>>> overlap. >>>> Segmentation fault 0 / 0 0% | >>>> >>>> And my YT script: >>>> >>>> from yt.mods import * >>>> pf = load("RD0002/RedDump0002", data_style = "enzo_packed_3d") >>>> pc = PlotCollection(pf, center = [0.5, 0.5, 0.5]) >>>> pc.add_particles(0, 0.5, p_size=1.0) >>>> pc.add_projection("particle_density_pyx", 0) >>>> pc.add_projection("particle_density_pyx", 1) >>>> pc.save("RD0002/Redshift100") >>>> >>>> Thanks in advance, >>>> Kai >>>> >>>> ---------------------------------------------------------------- >>>> This message was sent using IMP, the Internet Messaging Program. >>>> ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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units
by gso＠physics.ucsd.edu 11 Mar '10

11 Mar '10

When the line self["particle_velocity_x"] is called in HaloFinding.py, does it automatically give the number in CGS units already or is it in code units? It's used in calculating the rms velocity for each of the dark matter haloes, but it's subtracting centers and multiplying other values in code units I believe, just want to make sure the calculations are done in the same units. From G.S.

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Make Enzo Errors
by dlleuz＠xmission.com 10 Mar '10

10 Mar '10

Hi, I'm trying to install enzo (latest version from svn) and get an Error 127 ignored. It installs okay and runs some of the examples, but not yet others. Might this error be important and anyone know what it means? Thanks sincerely. R.Soares

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Error 127 attachment
by dlleuz＠xmission.com 10 Mar '10

10 Mar '10

Sorry I forgot to include the log for Error 127 trying to make Enzo, which is used for yt of course. Here it is. -R.Soares

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"yt load" command
by Matthew Turk 10 Mar '10

10 Mar '10

Hi everybody, I have gotten a bit tired of loading up parameter files by hand, so I've added a very simple command line to do this: yt load [your_parameter_file] will start up an IPython session with the parameter file you specify in the variable 'pf'. IPython has a lot of really great features: http://ipython.scipy.org/doc/stable/html/index.html , and we're going to see if we can get yt tab-completion and some other fun things implemented in the near future. I didn't back port this feature to 1.6, but if you're on trunk, it's on the latest revision. Best, Matt

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Mercurial
by dlleuz＠xmission.com 03 Mar '10

03 Mar '10

Hi all, I'm installing yt-1.6 using the install_script.sh on Ubuntu 9.04. It stops at "installing Mercurial". Is Mercurial necessary, also what is it? Attached is tail of installation log. Thanks for any help, sincerely. -rsoares

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Default Colormap change
by Matthew Turk 01 Mar '10

01 Mar '10

Hi all, Just a quick note: in r1649 of the trunk, we've changed the default colormap from "jet" to "algae", which is an alias for what used to be called "bds_highcontrast", a custom-designed colormap by Britton Smith. -Matt

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Dealing with HOP groups
by Agarwal, Shankar 01 Mar '10

01 Mar '10

Hi Stephen, I read http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2009-March/0001… Do you remember the cosmology parameters for your run: particles, grid, box, refinement, AMR ON or OFF ? I have run a 200 Mpc/h box, 512^3 particle, 512^3 grid, AMR-OFF simulation and I get about 30,000 halos using HOP. When I try to finding virial halos, I get only 500. I may have to increase the grid to 1024^3. Let me know how you got 40,000 virial halos. Thanks Shankar

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