Mailman 3 August 2012 - yt-dev

rockstar halo finder
by Stephen Skory 16 Aug '12

16 Aug '12

Hi all, I am trying to explore the rockstar halo finder within yt following the text Chris Moody added to the docs: https://bitbucket.org/yt_analysis/yt-doc/src/eb3c3f1f7552/source/analysis_m… The instructions include downloading a patched version of rockstar from this link: https://bitbucket.org/MatthewTurk/rockstar which gives me a "permission denied" message. I've poked around in yt, and I don't think that the rockstar code is replicated in there. Are the instructions wrong, or are the permissions incorrect on Matt's BB repo? I also noticed that in the rockstar documentation, it says "The yt installation allows the option to install and configure Rockstar appropriately" - but I can't find anything about rockstar in install_script.sh. Am I missing something? Thanks for the help! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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plot window preferences
by Sam Skillman 13 Aug '12

13 Aug '12

Hi all, As it currently stands, PlotWindow now saves with the bbox_inches='tight'. This can unfortunately lead to different images sizes based on whether or not the text labels and colorbar tick labels extend too far. This gets annoying if you want to make a movie with frames where the limits change. Would there be any objection to adding a **kwargs to the end of PW.save() that gets passed through to canvas.savefig? That way we can accept things like bbox_inches directly in the PW.save(). +/- 1 ? Sam

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yt for lagrangian hydro
by Matt Terry 13 Aug '12

13 Aug '12

Hi, I saw Matt's yt presentation at scipy. You've developed a cool tool. I'm covetous. I work with a 2D-RZ/3D-Cartesian Lagrangian hydrodynamics code ("Hydra"). The mesh is composed of logically rectangular blocks. Block boundaries can have reduced/enhanced connectivity zones, but nothing worse. How difficult do you think it would be to teach yt how work with Hydra meshes? -matt

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Problem with serialization and projections
by Michael Kuhlen 10 Aug '12

10 Aug '12

Hi I think I've found a bug with serialization and projections with a data_source. If I do a projection providing a data_source everything is fine: disk = pf.h.disk((0.5,0.5,0.5), (0,0,1), (10.0,'kpc'), (2.0,'kpc')) pc = PlotCollection(pf) pc.add_projection("NumberDensity","z",weight_field="Density", data_source=disk) But then, if I do the exact same projection without a data_source, it breaks with an error: 'No field named px'. The full traceback is at http://paste.yt-project.org/show/2637/. Note that if I first delete the .yt file, then the projection without data_source works just fine. Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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lost weak reference
by david collins 10 Aug '12

10 Aug '12

Hi, all-- Is there a way to reconstruct a bad data object? I'm making a bunch of clumps, but some how (unsure how right now) the weak reference to "data" on some of them is evaporating. Thanks, d. >>> the_clumps[1].data Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/dccollins/local2/src/yt-hg/yt/data_objects/data_containers.py", line 3006, in __repr__ s = "%s (%s): " % (self.__class__.__name__, self.pf) ReferenceError: weakly-referenced object no longer exists -- Sent from my computer.

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Success Story
by Christopher Moody 08 Aug '12

08 Aug '12

Hey guys, I just wanted to let everyone know that for the last few days I've been trying to pitch yt in 60-second plugs to a gang of hydroART simulation-analyzers. In my elevator pitch, they found the Reason GUI, natural AMR slicing, plots, etc., convincing reasons to use yt. Only time will tell if they choose the red pill, but I wanted to share a bit of success with y'all. chris

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Forthon issues
by Stephen Skory 08 Aug '12

08 Aug '12

Hi all, Some problems Sam was having with the fortan kdtree has alerted me to some necessary changes due to changes in Forthon. Two of them are simple. One is to remove a --with-numpy flag in the Makefile. The second is that the most recent version of Forthon (0.8.9) builds the fKDpy.so object in it's own build/lib.arch.../ directory, not in the same directory as the Makefile. This is easily fixed by a change to the setup.py file in yt/utilities. I will issue a PR for this depending on the discussion of the following issue. The not-simple change is that the newest Forthon setup.py is hard-coded to install the Forthon package for the system Python, regardless of which actual Python stack you're using, which is not convenient for our custom-curated yt stack. The fix is to simply remove the hard-coding. But I want to ask y'all what the best course forward from here is: A) ask the author to change it, B) make the change in the Forthon linked to in the install_script, or C) stick to the old version for now? Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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Some useful mercurial extensions
by Nathan Goldbaum 08 Aug '12

08 Aug '12

Hi all, Sam Skillman posted a link to a very useful listing of mercurial extensions on google+ from a stackoverflow discussion. They're so useful that I want to bring them to the attention of the yt and enzo development community. http://stackoverflow.com/questions/1869040/what-are-the-best-and-must-have-… To turn on any of the extensions, you'll need to add an [extensions] section to your hgrc (if it's not already there) and under that heading turn on the extensions you want to use. Here's what mine looks like right now: [extensions] mq = config = /u/ngoldbau/Tools/yt-x86_64/src/yt-supplemental/cedit hgbb = /u/ngoldbau/Tools/yt-x86_64/src/yt-supplemental/hgbb/hgbb.py hgext.extdiff = color = pager = fetch = graphlog = record = The color and pager extensions are particularly revolutionary for my usual mercurial workflow. Hope others find this as useful as I do :) Cheers, -Nathan

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Re: [yt-dev] [yt-users] Make projections for uniform grid FLASH4 data
by John ZuHone 07 Aug '12

07 Aug '12

Hi Suoqing, We have a patch for at least part of the problem you are seeing with 2D data. If you're on the development branch, try updating using "yt update." If the output of "yt instinfo" doesn't have the current version of the code as "a0d43ccae65d", then you'll have to manually pull as Matt had you do before: hg pull https://bitbucket.org/yt_analysis/yt hg up python2.7 setup.py develop This will fix the slice plots, but we've tried doing a projection plot using your data and the code segfaults. We will have to look into this a little more to see what is going on with that, but I'm sure it's a mistake on our end somewhere. We've talked about it on the dev side, and it is true that you should get the same thing with a slice and a projection for 2D data, except for the fact that the projected data will have been multiplied by the length of the domain in the z direction (which in your case appears to be the width of one cell), unless you have weighted the data by something. So my advice would be just to use slices for 2D data. Thanks for bringing all of this to our attention... we really want to make sure everyone's FLASH data is well-supported. Best, John Z On Aug 7, 2012, at 5:04 PM, Nathan Goldbaum wrote: > Hi Suoqing, > > John ZuHone is going to try to sort this out tonight. I think he'll let you know as soon as he figures out what went wrong. > > Cheers, > > Nathan > > On Aug 7, 2012, at 1:15 PM, Ji Suoqing wrote: > >> Hi Nathan, >> >> Sure! It just took several time for me to download from server and upload to dropbox. >> >> http://dl.dropbox.com/u/83265784/relax_hdf5_chk_0000 >> >> Thanks for your consideration and care! >> >> Best wishes, >> Suoqing >> >> 在 2012-8-7，下午4:03，Nathan Goldbaum <nathan12343(a)gmail.com> 写道： >> >>> I'm replying off-list because to minimize the number of messages to the rest of yt-users. >>> >>> Would you mind making your dataset available to me? It will make it much easier to figure out what's going wrong if I can directly reproduce the behavior you're seeing. >>> >>> Cheers, >>> >>> Nathan >>> >>> On Aug 7, 2012, at 12:57 PM, Ji Suoqing wrote: >>> >>>> Hi Matt, Hi John, >>>> >>>> I've tried slicing, and still got the same error: >>>> >>>>>>> from yt.mods import * >>>>>>> pf=load('relax_hdf5_chk_0000') >>>> yt : [INFO ] 2012-08-07 23:53:31,172 Parameters: current_time = 0.0 >>>> yt : [INFO ] 2012-08-07 23:53:31,172 Parameters: domain_dimensions = [512 256 1] >>>> yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] >>>> yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] >>>> yt : [INFO ] 2012-08-07 23:53:31,173 Parameters: cosmological_simulation = 0.0 >>>>>>> p=SlicePlot(pf, 'z', 'Density') >>>> yt : [INFO ] 2012-08-07 23:55:10,116 Adding unknown field fspd to list of fields >>>> yt : [INFO ] 2012-08-07 23:55:10,116 Adding unknown field spec to list of fields >>>> Traceback (most recent call last): >>>> File "<stdin>", line 1, in <module> >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 803, in __init__ >>>> slc = pf.h.slice(axis, center[axis], fields=fields) >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1042, in __init__ >>>> self._refresh_data() >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data >>>> self.get_data() >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 830, in get_data >>>> self._generate_coords() >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1076, in _generate_coords >>>> for grid in self._get_grids(): >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 900, in _get_grids >>>> return ObjectIterator(self, attr='_grids') >>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 102, in __init__ >>>> raise YTNoDataInObjectError(pobj) >>>> yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. It may lie on a grid face. Try offsetting slightly. >>>> >>>> And for John, I always use projection to deal with 2D AMR FLASH data and it works fine, because I suspect that projection will add all the data on different refinement level together. But I suspect slicing might not do exactly the same thing. And now for uniform grid data, both projection and slicing failed. >>>> >>>> All best, >>>> Suoqing >>>> >>>> >>>> 在 2012-8-7，下午3:42，John ZuHone <jzuhone(a)gmail.com> 写道： >>>> >>>>> Suoqing, >>>>> >>>>> Just a quick question... I notice that your dataset is 2D. Have you tried using a SlicePlot instead? If your dataset is 2D, projections and slices should be identical. >>>>> >>>>> I'm not saying that the projection should fail like it does, but I suspect that you probably would not have trouble with a slice and you would get the same result. >>>>> >>>>> Best, >>>>> >>>>> John Z >>>>> >>>>> On Aug 7, 2012, at 3:40 PM, Ji Suoqing wrote: >>>>> >>>>>> Ah, thanks a lot! With your suggestion I have axis ticks now. >>>>>> >>>>>> And the ug projection is still a problem. >>>>>> >>>>>> Best wishes, >>>>>> Suoqing >>>>>> >>>>>> 在 2012-8-7，下午3:34，Ji Suoqing <jisuoqing(a)gmail.com> 写道： >>>>>> >>>>>>> Hi Matt, >>>>>>> >>>>>>> Thanks for you response. I've tried: >>>>>>> >>>>>>>>>> from yt.mods import * >>>>>>>>>> pf=load('relax_hdf5_chk_0000') >>>>>>> yt : [INFO ] 2012-08-07 23:39:54,570 Parameters: current_time = 0.0 >>>>>>> yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_dimensions = [512 256 1] >>>>>>> yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] >>>>>>> yt : [INFO ] 2012-08-07 23:39:54,571 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] >>>>>>> yt : [INFO ] 2012-08-07 23:39:54,572 Parameters: cosmological_simulation = 0.0 >>>>>>>>>> p = ProjectionPlot(pf, "z", "Density") >>>>>>> yt : [INFO ] 2012-08-07 23:40:02,771 Adding unknown field fspd to list of fields >>>>>>> yt : [INFO ] 2012-08-07 23:40:02,772 Adding unknown field spec to list of fields >>>>>>> Traceback (most recent call last): >>>>>>> File "<stdin>", line 1, in <module> >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 875, in __init__ >>>>>>> proj = pf.h.proj(axis,fields,weight_field=weight_field,max_level=max_level,center=center) >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1697, in __init__ >>>>>>> self._initialize_source(source) >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1724, in _initialize_source >>>>>>> source = self.pf.h.all_data() >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 188, in all_data >>>>>>> pf.domain_left_edge, pf.domain_right_edge) >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3221, in __init__ >>>>>>> self._refresh_data() >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data >>>>>>> self.get_data() >>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2508, in get_data >>>>>>> raise YTNoDataInObjectError(self) >>>>>>> yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. >>>>>>> >>>>>>> All best, >>>>>>> Suoqing >>>>>>> >>>>>>> 在 2012-8-7，下午3:24，Matthew Turk <matthewturk(a)gmail.com> 写道： >>>>>>> >>>>>>>> Hi Suoqing, >>>>>>>> >>>>>>>> Could you try it with the ProjectionPlot call? It should look like this: >>>>>>>> >>>>>>>> p = ProjectionPlot(pf, "z", "Density") >>>>>>>> p.save() >>>>>>>> >>>>>>>> -Matt >>>>>>>> >>>>>>>> On Tue, Aug 7, 2012 at 3:14 PM, Ji Suoqing <jisuoqing(a)gmail.com> wrote: >>>>>>>>> Hi all, >>>>>>>>> >>>>>>>>> I'm trying to make projections for uniform grid FLASH4 data with the most updated YT, but there're errors when adding projections: >>>>>>>>> >>>>>>>>> yt : [WARNING ] 2012-08-07 23:13:56,239 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,244 Parameters: current_time = 0.0 >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_dimensions = [512 256 1] >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_left_edge = [ 1.50000000e+07 -6.55360000e+09 0.00000000e+00] >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: domain_right_edge = [ 2.62144000e+10 6.55360000e+09 1.74532925e-02] >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,245 Parameters: cosmological_simulation = 0.0 >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,587 Max Value is 2.46340e+06 at 38378027.3437500000000000 6400000.0000000000000000 0.5000000000000000 in grid FLASHGrid_0033 ([128 128 1]) at level 0 (1, 0, 0) >>>>>>>>> yt : [INFO ] 2012-08-07 23:13:56,587 Created plot collection with default plot-center = [13114700000.0, 0.0, 0.0087266462599716477] >>>>>>>>> Traceback (most recent call last): >>>>>>>>> File "proj.py", line 18, in <module> >>>>>>>>> p1 = pc.add_projection(my_var, 2) >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 784, in add_projection >>>>>>>>> **field_parameters) >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1697, in __init__ >>>>>>>>> self._initialize_source(source) >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 1724, in _initialize_source >>>>>>>>> source = self.pf.h.all_data() >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 188, in all_data >>>>>>>>> pf.domain_left_edge, pf.domain_right_edge) >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3221, in __init__ >>>>>>>>> self._refresh_data() >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 315, in _refresh_data >>>>>>>>> self.get_data() >>>>>>>>> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2508, in get_data >>>>>>>>> raise YTNoDataInObjectError(self) >>>>>>>>> yt.utilities.exceptions.YTNoDataInObjectError: The object requested has no data included in it. >>>>>>>>> >>>>>>>>> >>>>>>>>> And another separated question: how can I add axis ticks onto projection or slice plot to show the spacial scale? I suspect there should exist some easy way, but I failed to find it. >>>>>>>>> >>>>>>>>> Thanks for your care! >>>>>>>>> >>>>>>>>> All best, >>>>>>>>> Suoqing >>>>>>>>> _______________________________________________ >>>>>>>>> yt-users mailing list >>>>>>>>> yt-users(a)lists.spacepope.org >>>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>>> _______________________________________________ >>>>>>>> yt-users mailing list >>>>>>>> yt-users(a)lists.spacepope.org >>>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> yt-users mailing list >>>>>> yt-users(a)lists.spacepope.org >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>>> >>>>> _______________________________________________ >>>>> yt-users mailing list >>>>> yt-users(a)lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >> >

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inline profiles
by Stephen Skory 07 Aug '12

07 Aug '12

Hi all, this is about inline Enzo+yt, but since I think the solution might be on the yt end, I'm sending it here. I am attempting to profile halos located inline, and I am running into trouble when I attempt to profile over the 'TotalMassMsun' field. It is dying when it tries to access the 'Dark_Matter_Density' field, which I think it expects to be available, but isn't because Enzo only produces that when it writes to disk (AFAIK?). If this sounds correct to those in the know, I'd like to ask if anyone has a good idea how to get around this? Should I make a derived field (perhaps over-writing the built-in 'Dark_Matter_Density') using CICDeposit? I suppose I could try this solution first without emailing y'all, but I was thinking that if I/we find a working solution, it could be added to yt so the next person doesn't have to figure it out, so I'd like to minimize the false starts of poor/incorrect implementations. Thanks for your comments. -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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