Mailman 3 July 2017 - yt-users

installing astropy
by Stephanie Tonnesen 20 Jul '17

20 Jul '17

Hi yt-users! I have installed yt version 3.4-dev using miniconda. I did not originally choose to install astropy, but now I need it. Does anyone know how to add astropy to my current yt version? Thanks! Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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Demeshening: future of particles in yt
by Matthew Turk 19 Jul '17

19 Jul '17

Hi folks, Last week at SciPy, Nathan Goldbaum and Meagan Lang gave a talk about the "demeshening" project. This is the project they're working on to build out next-gen particle support in yt, based around removing the octree indexing and adding in bitmap indexing, and in the process getting a better representation of the particles. Anyhow, the talk is online and is really quite good, so I wanted to pass it along. It goes into some detail about what it means for people using yt, as well as the underlying machinery. https://www.youtube.com/watch?v=pkZgQIGac6I -Matt

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Error annotating particles
by José Mauricio Utreras 18 Jul '17

18 Jul '17

Hi yt-users, I'm using an old and simple script to overplot particles but now is not working. Cheers! José Utreras slc=yt.SlicePlot(ds, 'z','density', width=(25,'kpc')) slc.annotate_particles(width=20*kpc) ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self) 1006 try:-> 1007 callback(cbw) 1008 except YTDataTypeUnsupported as e: ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in _check_geometry(self, plot) 53 if supp is None or geom in supp:---> 54 return func(self, plot) 55 if cs in ("axis", "figure") and "force" not in supp: ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in __call__(self, plot) 1574 px, py = self.convert_to_plot(plot,-> 1575 [np.array(particle_x[gg][::self.stride]), 1576 np.array(particle_y[gg][::self.stride])]) ~/miniconda3/lib/python3.6/site-packages/yt/units/yt_array.py in __getitem__(self, item) 1162 def __getitem__(self, item):-> 1163 ret = super(YTArray, self).__getitem__(item) 1164 if ret.shape == (): TypeError: slice indices must be integers or None or have an __index__ method During handling of the above exception, another exception occurred: YTPlotCallbackError Traceback (most recent call last)~/miniconda3/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj) 334 method = get_real_method(obj, self.print_method) 335 if method is not None:--> 336 return method() 337 return None 338 else: ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_container.py in newfunc(*args, **kwargs) 76 # it is the responsibility of _setup_plots to 77 # call args[0].run_callbacks()---> 78 args[0]._setup_plots() 79 rv = f(*args, **kwargs) 80 return rv ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in _setup_plots(self) 954 955 self._set_font_properties()--> 956 self.run_callbacks() 957 self._plot_valid = True 958 ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self) 1011 six.reraise(YTPlotCallbackError, 1012 YTPlotCallbackError(callback._type_name, e),-> 1013 sys.exc_info()[2]) 1014 for key in self.frb.keys(): 1015 if key not in keys: ~/miniconda3/lib/python3.6/site-packages/six.py in reraise(tp, value, tb) 683 value = tp() 684 if value.__traceback__ is not tb:--> 685 raise value.with_traceback(tb) 686 raise value 687 ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self) 1005 callback = CallbackMaker(*args[1:], **kwargs) 1006 try:-> 1007 callback(cbw) 1008 except YTDataTypeUnsupported as e: 1009 six.reraise(YTDataTypeUnsupported, e) ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in _check_geometry(self, plot) 52 cs = getattr(self, "coord_system", None) 53 if supp is None or geom in supp:---> 54 return func(self, plot) 55 if cs in ("axis", "figure") and "force" not in supp: 56 return func(self, plot) ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in __call__(self, plot) 1573 if gg.sum() == 0: return 1574 px, py = self.convert_to_plot(plot,-> 1575 [np.array(particle_x[gg][::self.stride]), 1576 np.array(particle_y[gg][::self.stride])]) 1577 plot._axes.scatter(px, py, edgecolors='None', marker=self.marker, ~/miniconda3/lib/python3.6/site-packages/yt/units/yt_array.py in __getitem__(self, item) 1161 1162 def __getitem__(self, item):-> 1163 ret = super(YTArray, self).__getitem__(item) 1164 if ret.shape == (): 1165 return YTQuantity(ret, self.units, bypass_validation=True) YTPlotCallbackError: annotate_particles callback failed with the following error: slice indices must be integers or None or have an __index__ method

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error
by Cynthia Saad (Student) 17 Jul '17

17 Jul '17

dear all i am using yt for enzo. my script reads: import yt # Load the dataset. ds = yt.load("~/enzo/run/CosmologySimulation/AMRCosmology/DD0001/DD0001") # Create a 1 Mpc radius sphere, centered on the max density. sp = ds.sphere("max", (0.1, "Mpc")) # Use the total_quantity derived quantity to sum up the # values of the cell_mass and particle_mass fields # within the sphere. baryon_mass, particle_mass = sp.quantities.total_quantity(["cell_mass", "particle_mass"]) print("Total mass in sphere is %0.3e Msun (gas = %0.3e Msun, particles = %0.3e Msun)" % \ ((baryon_mass + particle_mass).in_units('Msun'), \ baryon_mass.in_units('Msun'), particle_mass.in_units('Msun'))) ----------- the error i am getting is: ~/enzo/run/CosmologySimulation/AMRCosmology$ python trial.py Traceback (most recent call last): File "trial.py", line 4, in <module> ds = yt.load("~/enzo/run/CosmologySimulation/AMRCosmology/DD0001/DD0001") File "/usr/local/lib/python2.7/dist-packages/yt/convenience.py", line 79, in load if c._is_valid(*args, **kwargs): candidates.append(n) File "/usr/local/lib/python2.7/dist-packages/yt/frontends/flash/data_structures.py", line 493, in _is_valid fileh = HDF5FileHandler(args[0]) File "/usr/local/lib/python2.7/dist-packages/yt/utilities/file_handler.py", line 22, in __init__ self.handle = h5py.File(filename, 'r') File "/usr/local/lib/python2.7/dist-packages/yt/utilities/on_demand_imports.py", line 31, in __call__ raise self.error ImportError: This functionality requires the h5py package to be installed. ---------------- is my script outdated, there is something wrong with my installation or deficiencies in the python libraries? thank you cynthia

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[YT-USERS] Incoherence when ploting a slice - from FLASH simulation
by Gabriel RIGON 15 Jul '17

15 Jul '17

Dear all, I recently start to work with yt to analyze my FLASH simulation. The output of those simulation is an hdf5 file. When I try to plot a slice of my simulation, some weird lines appear on it. Here is an example of the python script and the results it leads to. """ import yt ds = yt.load("lasslab_hdf5_plt_cnt_0000.hdf5") yt.SlicePlot(ds, 'z', "dens").show() [cid:972219b9-edbb-4265-81cf-9a07e61cf360] """ Actually they also appear went plotting the results of a frb of a slice (even when I try to plot the x or y coordinate in 2d). Do you have any idea of the reason for such lines, or a solution for my problem? Best regards, Gabriel Rigon

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Re: [yt-users] accessing single elements of data when defining a new field
by sacielo 14 Jul '17

14 Jul '17

Thanks Matthew for your reply, the general problem of doing that is that the 'data' structure can point to arrays of 1, 2 or 3 dimensions, so it's difficult to loop over it. I ended up solving the problem in a better way: I switched to a scipy RectBivariateSpline interpolator, rather than a simpler interp2d object. Now I no more need to loop on the single elements, and can pass the full arrays. To get the numerical array, now I could simply use data['mydata'].value (I had to reshape it to a 1D array, but that was easy). Thank you anyway! Best, On Wed, Jul 12, 2017 at 6:14 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: accessing single elements of data when defining a new > field (Matthew Turk) > 2. Re: IO error (Britton Smith) > 3. Re: Field extraction from arbitrary grids (Carla Bernhardt) > 4. 3-D Mass power spectra (???) > 5. Re: 3-D Mass power spectra (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Jul 2017 07:16:20 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] accessing single elements of data when > defining a new field > Message-ID: > <CALO3=5GQeESENDeFQR70aeE9EtcNOcwUUrhxJYN_9+PhyPz= > oA(a)mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi Salvatore, > > This is odd -- I believe that it should work as you have written it. > Can you describe how it fails? And, what happens if instead of doing > > for ii in range(0, len(t)): > > you did something like: > > for val in t: > > and then operated on val? > > On Tue, Jul 11, 2017 at 4:59 AM, sacielo <sacielo(a)gmail.com> wrote: > > Hello > > > > I am trying to define a new field for a grid simulation (using ramses, > if it > > matters), basically an estimate of radiative cooling in a simulation that > > does not include that. > > > > I find myself to perform a 2D interpolation in a table (cooling rate > given > > temperature and metal content), then I wish to save this as a new field. > I > > am using a scipy 2D interpolator in order to do so. The problem is that > for > > the interpolation I need to access the single elements in the temperature > > and metal fields, within the function I use to define a new dataset > > (unfortunately, I am forced to loop on the fields). > > > > Now, I can't understand how to do that from the "data" and "field" > arguments > > of the functions. > > > > Something like > > t = data['temperature'] > > for ii in range(0, len(t)): > > print t[ii] > > > > fails (t[ii] is a complex array itself) > > > > t.base() and t.item() or t[ii].item() > > > > fail as well.... > > > > > > Any idea? > > > > Thank you! > > > > > > -- > > Salvatore > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Jul 2017 11:09:12 -0700 > From: Britton Smith <brittonsmith(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] IO error > Message-ID: > <CABfs61k3p07Yfcze8Jrf3-wjwfe38nWN5Yb1vv1cnWANi-m47Q@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > I just wanted to provide some resolution to this issue. The issue had to > do with some problems that have cropped up when trying to read hdf5 string > attributes in Python 3. You wouldn't see this if you were still using > Python 2. This has been resolved with the following pull request, which > has already been accepted: > https://github.com/yt-project/yt/pull/1487 > > Britton > > On Mon, Jul 10, 2017 at 1:13 PM, Britton Smith <brittonsmith(a)gmail.com> > wrote: > > > Hi Nick, > > > > This is a bit puzzling since I think there have been relatively few > > changes to the halo catalog frontend responsible for loading that data. > > That said, I would be more than happy to take a look as I am responsible > > for much of this code. Would you be able to share either 1) this dataset > > that is failing to load or 2) a script that uses example data that I can > > run to reproduce this? > > > > Britton > > > > On Mon, Jul 10, 2017 at 8:53 AM, Nick Gnedin <ngnedin(a)gmail.com> wrote: > > > >> > >> Folks, > >> > >> I have encountered a bizarre IO error. I am reading a file previously > >> created by yt HOP halo finder on two separate machines. The file reads > >> correctly on the machine it was created on, but on another machine with > the > >> most recent anaconda install (yt 3.3.5) the format is not recognized. > Both > >> machines are little endian. Is there any way to get more info on what yt > >> does not like about that file? > >> > >> yt : [ERROR ] 2017-07-10 10:46:00,454 Couldn't figure out output type > >> for hop.0.h5 > >> Traceback (most recent call last): > >> File "hmf.py", line 14, in <module> > >> Plot("hop.0.h5",color="b") > >> File "hmf.py", line 8, in Plot > >> my_halos = load(file) > >> File "/ext/anaconda3/lib/python3.6/site-packages/yt/convenience.py", > >> line 98, in load > >> raise YTOutputNotIdentified(args, kwargs) > >> yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('hop.0.h5',) > >> {}, but could not load! > >> > >> Here is the script (taken form your examples): > >> > >> > >> import yt > >> from yt.mods import * > >> from yt.analysis_modules.halo_mass_function.api import * > >> import matplotlib.pyplot as plt > >> > >> def Plot(file,color="r"): > >> my_halos = load(file) > >> hmf = HaloMassFcn(halos_ds=my_halos) > >> plt.loglog(hmf.masses_analytic, hmf.n_cumulative_analytic,colo > >> r="orange",linewidth=3) > >> plt.loglog(hmf.masses_sim, hmf.n_cumulative_sim,color=col > >> or,linewidth=3) > >> > >> Plot("hop.0.h5",color="b") > >> > >> > >> Thank you for your advice, > >> > >> Nick Gnedin > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170711/19feaa01/attachment-0001.htm> > > ------------------------------ > > Message: 3 > Date: Wed, 12 Jul 2017 12:35:14 +0200 > From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Field extraction from arbitrary grids > Message-ID: > <CAKQMXAWJWUANaiSVaMBoBMEcPKST+UUN--4QLj_nLwEDKV7q2Q@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Matthew, > > Thank you for your reply. I was using yt Version 3.2.3 and am working out > some installation issues on our server with version 3.3.5. As for the type > of data, I have an enzo simulation with static nested grids as well as up > to 6 levels AMR grids. I will have to get back to you once I get past the > issues with the newest installation of yt.... Thanks for the initial > pointers. > > Cheers, > Carla > > 2017-07-11 14:15 GMT+02:00 Matthew Turk <matthewturk(a)gmail.com>: > > > Hi Carla, > > > > Interesting. It's possible, for the call to "temperature" (which > > raises NotImplementedError) that the version of yt you're on doesn't > > yet support mesh fields in arbitrary grids; that was added reasonably > > recently. For the others, I'm not totally sure why it's breaking -- > > which version of yt are you using, and what type of data? It may just > > be that they aren't deposit fields. In that case, try explicitly > > stating obj["gas","temperature"] or obj["gas","HI_Density"]. It may > > also be that the aliasing is getting in the way, in which case instead > > of "HI_Density" you might need to try "Hp0_density". > > > > On Tue, Jul 11, 2017 at 5:42 AM, Carla Bernhardt > > <carla.j.bernhardt(a)gmail.com> wrote: > > > Dear yt-users, > > > > > > I am trying to extract a unigrid data cube within a specific region and > > > specified dimensions, thus I am using arbitrary_grid(), however, beyond > > the > > > example given in the docs, my field extractions all fail. I would like > to > > > extract temperature, HI_Density and HII_Density. Here is a snippet from > > my > > > code: > > > > > > obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) > > > print(obj["deposit", "all_density"]) > > > print(obj["temperature"]) > > > print(obj["HI_Density"]) > > > > > > The line print(obj["deposit", "all_density"]) works, but the two lines > > after > > > both fail. Here is the traceback from the temperature, and I even tried > > out > > > deposited temperature and deposited HI_Density. Am I formatting this > > > incorrectly, or is there a different way to extract the fields? > > > > > > Kind regards, > > > Carla Bernhardt > > > PhD Student > > > ZAH Institut f?r Theoretische Astrophysik > > > Universit?t Heidelberg > > > > > > _______________________________________________ > > > 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170712/a46e0643/attachment-0001.htm> > > ------------------------------ > > Message: 4 > Date: Thu, 13 Jul 2017 00:10:02 +0800 > From: ??? <setsuna(a)phys.tw> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] 3-D Mass power spectra > Message-ID: > <CAEtGJOz5LssuwrWmuXSYO+u77DPaW2v5yPM2TGFg+CYP2AV+7A@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear yt > > Can current yt calculate 3-D Mass power spectra? I checked the website but > I didn't find any information. I think calculating 3-D Mass power > spectra is a very useful for cosmological simulations. So I guess maybe yt > supports this function now....? > > Thanks in advance > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170713/a3c9b005/attachment-0001.htm> > > ------------------------------ > > Message: 5 > Date: Wed, 12 Jul 2017 11:13:50 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] 3-D Mass power spectra > Message-ID: > <CAJXewO=CQ3+PKt_jL9QBPvYd4g7hc7VrKLBD01W33u9jX > vg7gw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > We have an example in our docs that shows how to create a kinetic energy > power spectrum with the numpy FFT: > > http://yt-project.org/doc/cookbook/calculating_information.html#making-a- > turbulent-kinetic-energy-power-spectrum > > I think this could be adapted for your needs. > > Right now there isn't an analysis routine explicitly for computing power > spectra in yt. If someone wanted to add it (or just wanted to add more > examples to the docs of how to compute power spectra using e.g. pyfftw) I > think that would be a very welcome contribution. > > -Nathan > > On Wed, Jul 12, 2017 at 11:10 AM, ??? <setsuna(a)phys.tw> wrote: > > > Dear yt > > > > Can current yt calculate 3-D Mass power spectra? I checked the website > but > > I didn't find any information. I think calculating 3-D Mass power > > spectra is a very useful for cosmological simulations. So I guess maybe > yt > > supports this function now....? > > > > Thanks in advance > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170712/c8e1fe3f/attachment.htm> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 113, Issue 17 > ***************************************** > -- Salvatore

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IO error
by Nick Gnedin 11 Jul '17

11 Jul '17

Folks, I have encountered a bizarre IO error. I am reading a file previously created by yt HOP halo finder on two separate machines. The file reads correctly on the machine it was created on, but on another machine with the most recent anaconda install (yt 3.3.5) the format is not recognized. Both machines are little endian. Is there any way to get more info on what yt does not like about that file? yt : [ERROR ] 2017-07-10 10:46:00,454 Couldn't figure out output type for hop.0.h5 Traceback (most recent call last): File "hmf.py", line 14, in <module> Plot("hop.0.h5",color="b") File "hmf.py", line 8, in Plot my_halos = load(file) File "/ext/anaconda3/lib/python3.6/site-packages/yt/convenience.py", line 98, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('hop.0.h5',) {}, but could not load! Here is the script (taken form your examples): import yt from yt.mods import * from yt.analysis_modules.halo_mass_function.api import * import matplotlib.pyplot as plt def Plot(file,color="r"): my_halos = load(file) hmf = HaloMassFcn(halos_ds=my_halos) plt.loglog(hmf.masses_analytic, hmf.n_cumulative_analytic,color="orange",linewidth=3) plt.loglog(hmf.masses_sim, hmf.n_cumulative_sim,color=color,linewidth=3) Plot("hop.0.h5",color="b") Thank you for your advice, Nick Gnedin

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accessing single elements of data when defining a new field
by sacielo 11 Jul '17

11 Jul '17

Hello I am trying to define a new field for a grid simulation (using ramses, if it matters), basically an estimate of radiative cooling in a simulation that does not include that. I find myself to perform a 2D interpolation in a table (cooling rate given temperature and metal content), then I wish to save this as a new field. I am using a scipy 2D interpolator in order to do so. The problem is that for the interpolation I need to access the single elements in the temperature and metal fields, within the function I use to define a new dataset (unfortunately, I am forced to loop on the fields). Now, I can't understand how to do that from the "data" and "field" arguments of the functions. Something like t = data['temperature'] for ii in range(0, len(t)): print t[ii] fails (t[ii] is a complex array itself) t.base() and t.item() or t[ii].item() fail as well.... Any idea? Thank you! -- Salvatore

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Yt line query: Segmentation fault (core dumped)
by Chongchong He 10 Jul '17

10 Jul '17

Dear Sir/Madam, I came into a problem when using yt to deal with my RAMSES data. The procedures to produce the error and some info is as follow. Do you have any idea what’s going wrong here? I use the data from yt-project.org/data/ <http://yt-project.org/data/>, in the row of ramses_extra_fields_small. The python code that generates this issue is uploaded to http://paste.yt-project.org/show/7203/ <http://paste.yt-project.org/show/7203/> On macOS Sierra 10.12.5 The print-out message: yt : [INFO ] 2017-07-09 14:06:59,521 Parameters: current_time = 0.03744727779 yt : [INFO ] 2017-07-09 14:06:59,521 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2017-07-09 14:06:59,521 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2017-07-09 14:06:59,521 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2017-07-09 14:06:59,521 Parameters: cosmological_simulation = 0 Segmentation fault: 11 Some info: ~$ yt version yt module located at: /Users/chongchonghe/local/yt-conda/lib/python2.7/site-packages The current version of yt is: --- Version = 3.4-dev --- ~$ python --version Python 2.7.13 On Red Hat Enterprise Linux Server 7.3 The print-out message: yt : [INFO ] 2017-07-09 14:19:10,883 Parameters: current_time = 0.03744727779 yt : [INFO ] 2017-07-09 14:19:10,883 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2017-07-09 14:19:10,884 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2017-07-09 14:19:10,884 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2017-07-09 14:19:10,884 Parameters: cosmological_simulation = 0 Segmentation fault (core dumped) Some info: startrek% yt version yt module located at: /startrek/chongchong/codes/yt-conda/lib/python2.7/site-packages The current version of yt is: --- Version = 3.3.5 --- startrek% python --version Python 2.7.13 :: Continuum Analytics, Inc. Many thanks, ChongChong He Graduate Student, Department of Astronomy University of Maryland, College Park, 20742, MD

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IO error
by Nick Gnedin 10 Jul '17

10 Jul '17

Folks, I am getting IO errors in the following simple script: import yt from yt.analysis_modules.halo_analysis.api import HaloCatalog root = "/data/gnedin/REI/D/M/Cai.B20.N128L2.sf=1.5_uv=0.15_bw=10_res=100.WC1.WDM=3.0/A/" d = yt.load(root+"rei20_a0.1553/rei20_a0.1553.art") hc = HaloCatalog(data_ds=d,finder_method='hop',output_dir=root+"a=0.1553") hc.create() I wonder if anyone knows what a "key error" is. Here is the stdout: ~/ART/REI/PLOT >/data/gnedin/soft/anaconda3/bin/python3 hfc.py yt : [WARNING ] 2017-07-06 13:45:37,086 DeltaDC != 0, which implies auni != abox. Be sure you understand which expansion parameter is appropriate for your use! (Gnedin, Kravtsov, & Rudd 2011) yt : [INFO ] 2017-07-06 13:45:37,103 Parameters: current_time = 1057933112.4042035 yr yt : [INFO ] 2017-07-06 13:45:37,103 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2017-07-06 13:45:37,104 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: domain_right_edge = [ 128. 128. 128.] yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: cosmological_simulation = True yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: current_redshift = 5.440284424726534 yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: omega_lambda = 0.6964000165462494 yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: omega_matter = 0.3035999834537506 yt : [INFO ] 2017-07-06 13:45:37,105 Parameters: hubble_constant = 0.6814000010490417 yt : [WARNING ] 2017-07-06 13:45:38,199 dm_only is deprecated. Use ptype to specify a particle type, instead. yt : [WARNING ] 2017-07-06 13:45:38,200 No particle_type, no creation_time, so not distinguishing. yt : [INFO ] 2017-07-06 13:46:54,456 Created 2048 chunks for ARTIO Traceback (most recent call last): File "hfc.py", line 9, in <module> hc.create() File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 334, in create self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 302, in barrierize return func(*args, **kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 403, in _run self.halos_ds = self.finder_method(self.data_ds) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 44, in __call__ return self.function(ds, *self.args, **self.kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_finding_methods.py", line 51, in _hop_method halo_list = HOPHaloFinder(ds, **finder_kwargs) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_finding/halo_objects.py", line 1504, in __init__ self.comm.mpi_allreduce((self._data_source['all', "particle_mass"][select].in_units('Msun')).sum(dtype='float64'), op='sum') File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 272, in __getitem__ self.get_data(f) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/data_objects/data_containers.py", line 1186, in get_data particles, self, self._current_chunk) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/geometry/geometry_handler.py", line 227, in _read_particle_fields fields_to_read) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/utilities/io_handler.py", line 179, in _read_particle_selection for field_r, vals in self._read_particle_fields(chunks, ptf, selector): File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/frontends/artio/io.py", line 63, in _read_particle_fields rv = dict(**subset.fill_particles(fields)) File "/data/gnedin/soft/anaconda3/lib/python3.6/site-packages/yt/frontends/artio/data_structures.py", line 107, in fill_particles count += species_data[i, f].size KeyError: (0, 'MASS')

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