Mailman 3 June 2016 - yt-dev

Boolean data objects in yt-3
by Brian O'Shea July 1, 2016

July 1, 2016

Hi folks, I've stumbled across across a research task that could really use yt's Boolean data object feature, and according to the documentation it is not implemented in yt-3. Have boolean data objects been replaced by something else? I know there are various filtering methods in yt, but what I really need to do is spatial filtering (i.e., data in a sphere with some chunks of the sphere excised). In principle I'd be happy to take a crack at re-implementing it, although I might need some help. Could somebody give me a sense of why it wasn't ported to yt-3 when the changeover was made? Thanks, Brian

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Issue #1237: HaloMassFcn units (or coments) inconsistent (yt_analysis/yt)
by spthm June 29, 2016

June 29, 2016

New issue 1237: HaloMassFcn units (or coments) inconsistent https://bitbucket.org/yt_analysis/yt/issues/1237/halomassfcn-units-or-comen… spthm: Disclaimer: I'm not particularly experienced in HMFs. The below may not actually be a bug (just confusing/incorrect comments); if it is, I imagine it relates to issue #1228. It should possibly be a comment on that issue, but I can't confirm the two are related. For reference, I'm going to link to the current stable yt, 3.2.3. Based on comments in [`halo_mass_function.py`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py), I do not believe the stated output units are correct. [`halo_mass_function.py:403`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py-403) multiplies `rho_crit_g_cm3_h2` by `hubble0**2`, resulting in units of `Msolar/Mpc^3` for `rho0` _if the comment at [`physical_ratios.py:103`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/utilities/physical_ratios.py?at=yt&fileviewer=file-view-default#physical_ratios.py-103) is to be believed_. But line 402 directly above states `rho0 in units of h^2 Msolar/Mpc^3`. This error carries through to line [`halo_mass_function.py:432`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py-432). It is claimed that `dndM_dM_analytic` has units of `h^3`, but it is actually `h`. Finally, at [`halo_mass_function.py:436`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py-436) we multiply through by `h^3`, resulting units of `h^-2` for `dndM_dM_analytic` and `n_cumulative_analytic` (while it is claimed that all `h` are cancelled out). Note that [`halo_mass_function.py:368`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py-368) has a similar issue, in that `h^2` units are claimed, but `rho0` has no `h` dependence. The proceeding usage of `rho0` at [`halo_mass_function.py:390`](https://bitbucket.org/yt_analysis/yt/src/bdea84d950999973d7b80cba34acc4c70b62a925/yt/analysis_modules/halo_mass_function/halo_mass_function.py?at=stable&fileviewer=file-view-default#halo_mass_function.py-390) implies that `rho0` indeed should have units `h^2` to achieve a `h^-1` for `thisradius`. I think this has a non-trivial impact on the values in `sigmaarray`, but I gave up trying to track it. The masses do not appear to be affected, but both analytic output arrays seem to have erroneous factors of `h`, and I believe the sigma values are also computed with incorrect `R` values. Since I gave up trying to track how incorrect `R` impacts `sigma`, I don't know if this all agrees with the behaviour described by @ioodderskov in #1228. All that said, if I make the obvious change of _not_ multiplying `rho` by `hubble0**2`, the analytic fits do a much worse job of fitting haloes in some of my Gadget-2 snapshots, whereas before agreement with P-S was very good. But I have no idea if this is a fluke, and the simulations are faulty, or whether all of the above is a misunderstanding on my part. The multiplication by `hubble0**2` was introduced in ab0d4e0.

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PR review hangout
by Nathan Goldbaum June 29, 2016

June 29, 2016

Hi all, Let's have a PR review hangout this week. I've scheduled it for Wednesday at 1:00 PM CDT: https://plus.google.com/b/107728486871834552760/events/cvj9s3g32u526cjj8nj1… Let me know if that time is bad for anyone that would like to attend so we can reschedule. -Nathan

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Issue #1236: While installing yt through script (yt_analysis/yt)
by Damodar Rajbhandari June 27, 2016

June 27, 2016

New issue 1236: While installing yt through script https://bitbucket.org/yt_analysis/yt/issues/1236/while-installing-yt-throug… Damodar Rajbhandari: I have tried to install yt for the first time in my Ubuntu 16.04 LTS but i got an error "Import Error: cannot import name HTTPS Handler". Here are some lines from the yt_install.log ..... using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: No module named _ssl! using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: No module named _ssl! abort: repository /home/field/yt-x86_64/src/yt-hg/ not found! 2016-06-26 19:49:49 URL:https://bootstrap.pypa.io/get-pip.py [1524722/1524722] -> "get-pip.py" [1] Traceback (most recent call last): File "get-pip.py", line 19177, in <module> main() File "get-pip.py", line 194, in main bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpzwM52k/pip.zip/pip/__init__.py", line 16, in <module> File "/tmp/tmpzwM52k/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpzwM52k/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpzwM52k/pip.zip/pip/wheel.py", line 39, in <module> File "/tmp/tmpzwM52k/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpzwM52k/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler using https://bitbucket.org/yt_analysis/yt-supplemental/ sending capabilities command abort: No module named _ssl! using https://bitbucket.org/yt_analysis/yt/ sending capabilities command abort: No module named _ssl! abort: repository /home/field/yt-x86_64/src/yt-hg/ not found! 2016-06-26 20:05:41 URL:https://bootstrap.pypa.io/get-pip.py [1524722/1524722] -> "get-pip.py.1" [1] Traceback (most recent call last): File "get-pip.py", line 19177, in <module> main() File "get-pip.py", line 194, in main bootstrap(tmpdir=tmpdir) File "get-pip.py", line 82, in bootstrap import pip File "/tmp/tmpJkD7Nt/pip.zip/pip/__init__.py", line 16, in <module> File "/tmp/tmpJkD7Nt/pip.zip/pip/vcs/subversion.py", line 9, in <module> File "/tmp/tmpJkD7Nt/pip.zip/pip/index.py", line 30, in <module> File "/tmp/tmpJkD7Nt/pip.zip/pip/wheel.py", line 39, in <module> File "/tmp/tmpJkD7Nt/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in <module> File "/tmp/tmpJkD7Nt/pip.zip/pip/_vendor/distlib/compat.py", line 31, in <module> ImportError: cannot import name HTTPSHandler Then, i try to install by typing sudo apt-get install python-yt. But i don't know what was going there! So, again i tried, its showed me an error "make: *** [install-recursive] Error 1". Here are some lines from another yt_install.log ...... In file included from h5tools_dump.c:31:0: ../../src/H5private.h:1529:14: warning: ISO C90 does not support '__func__' predefined identifier [-Wpedantic] #define FUNC __func__ ^ h5tools_error.h:71:49: note: in expansion of macro 'FUNC' H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, maj_id, min_id, str); \ ^ h5tools_error.h:101:5: note: in expansion of macro 'HERROR' HERROR(H5E_tools_g, min_id, str); \ ^ h5tools_dump.c:2688:9: note: in expansion of macro 'H5E_THROW' H5E_THROW(FAIL, H5E_tools_min_id_g, "Could not close datatype's super class"); ^ h5tools_dump.c: In function 'h5tools_dump_comment': h5tools_dump.c:3460:59: warning: conversion to 'size_t {aka long unsigned int}' from 'ssize_t {aka long int}' may change the sign of the result [-Wsign-conversion] cmt_bufsize = H5Oget_comment(obj_id, comment, cmt_bufsize); ^ h5tools_dump.c: In function 'h5tools_dump_attribute': h5tools_dump.c:3489:39: warning: unused parameter 'oid' [-Wunused-parameter] h5tools_context_t *ctx, hid_t oid, const char *attr_name, hid_t attr_id, ^ h5tools_dump.c: In function 'h5tools_print_packed_bits': h5tools_dump.c:3628:48: warning: ISO C90 does not support 'long long' [-Wlong-long] packed_bits_size = 8 * sizeof(long long); ^ h5tools_dump.c:3631:57: warning: ISO C90 does not support 'long long' [-Wlong-long] packed_bits_size = 8 * sizeof(unsigned long long); ^ Makefile:553: recipe for target 'h5tools_dump.lo' failed make[2]: *** [h5tools_dump.lo] Error 1 make[2]: Leaving directory '/home/field/yt-x86_64/src/hdf5-1.8.11/tools/lib' Makefile:497: recipe for target 'install-recursive' failed make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory '/home/field/yt-x86_64/src/hdf5-1.8.11/tools' Makefile:539: recipe for target 'install-recursive' failed make: *** [install-recursive] Error 1 Can anyone can help me out from this issue.

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Some yt related services are unavailable
by Kacper Kowalik June 23, 2016

June 23, 2016

Hi all, This morning around 7am fido - our server located @ NCSA - was compromised and used in DDoS attack on some random ip in China. As soon as the secops noticed unusual behaviour they shut it down. Fido serves as reverse proxy for various services related to yt. As long as it's down anything that we were hosting at *.hub.yt and *.use.yt won't be available. This also affects: blog.yt-project.org and tests.yt-project.org. At this time I don't have any ETA on when the services will be brought back to life. I'll notify you as soon as there's any progress. I'm sorry for all the inconvenience this situation creates. Kacper

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Issue #1235: ytdata reloaded projection of ('gas', 'density') cannot create the ('gas', 'cell_mass') field (yt_analysis/yt)
by Nathan Goldbaum June 23, 2016

June 23, 2016

New issue 1235: ytdata reloaded projection of ('gas', 'density') cannot create the ('gas', 'cell_mass') field https://bitbucket.org/yt_analysis/yt/issues/1235/ytdata-reloaded-projection… Nathan Goldbaum: The following script illustrates the issue: ``` import yt ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030') prj = ds.proj(['density', 'radius'], 0) prj.save_as_dataset() ds2 = yt.load('galaxy0030_proj.h5') ad = ds2.all_data() ad['cell_mass'] ``` This produces the following traceback: ``` ValueError Traceback (most recent call last) /Users/goldbaum/Documents/yt-hg/yt/mods.pyc in <module>() 3 ds2 = yt.load('galaxy0030_proj.h5') 4 ad = ds2.all_data() ----> 5 ad['cell_mass'] /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 270 return self.field_data[f] 271 else: --> 272 self.get_data(f) 273 # fi.units is the unit expression string. We depend on the registry 274 # hanging off the dataset to define this unit object. /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields) 1188 1189 fields_to_generate += gen_fluids + gen_particles -> 1190 self._generate_fields(fields_to_generate) 1191 for field in list(self.field_data.keys()): 1192 if field not in ofields: /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 1208 fi = self.ds._get_field_info(*field) 1209 try: -> 1210 fd = self._generate_field(field) 1211 if fd is None: 1212 raise RuntimeError /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in _generate_field(self, field) 307 tr = self._generate_particle_field(field) 308 else: --> 309 tr = self._generate_fluid_field(field) 310 if tr is None: 311 raise YTCouldNotGenerateField(field, self.ds) /Users/goldbaum/Documents/yt-hg/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field) 327 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 328 else: --> 329 rv = finfo(gen_obj) 330 return rv 331 /Users/goldbaum/Documents/yt-hg/yt/fields/derived_field.pyc in __call__(self, data) 196 "for %s" % (self.name,)) 197 with self.unit_registry(data): --> 198 dd = self._function(self, data) 199 for field_name in data.keys(): 200 if field_name not in original_fields: /Users/goldbaum/Documents/yt-hg/yt/fields/fluid_fields.pyc in _cell_mass(field, data) 58 59 def _cell_mass(field, data): ---> 60 return data[ftype, "density"] * data[ftype, "cell_volume"] 61 62 registry.add_field((ftype, "cell_mass"), /Users/goldbaum/Documents/yt-hg/yt/units/yt_array.pyc in __mul__(self, right_object) 956 """ 957 ro = sanitize_units_mul(self, right_object) --> 958 return super(YTArray, self).__mul__(ro) 959 960 def __rmul__(self, left_object): ValueError: operands could not be broadcast together with shapes (41119,) (55672,) ```

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Issue #1234: Volume rendering example in "loading generic array data" notebook needs to be updated (yt_analysis/yt)
by Nathan Goldbaum June 19, 2016

June 19, 2016

New issue 1234: Volume rendering example in "loading generic array data" notebook needs to be updated https://bitbucket.org/yt_analysis/yt/issues/1234/volume-rendering-example-i… Nathan Goldbaum: Right now this documentation page contains runtime errors because it uses the old volume rendering interface. http://yt-project.org/docs/dev/examining/generic_array_data.html

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Pretty visuals?
by Nathan Goldbaum June 18, 2016

June 18, 2016

Hi all, Does anyone have any pretty visuals (be it images, plots, or movies) that they wouldn't mind me showing off at a yt tutorial? Of course you will be duly credited and praised for your awesome visuals :) I'll be giving the tutorial at McMaster this weekend as part of a python for astronomers workshop before the Great Lakes Cosmology workshop. Thanks! -Nathan

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Issue #1233: Add basic sanity checks to ensure yt installation is working after install script finishes (yt_analysis/yt)
by Nathan Goldbaum June 17, 2016

June 17, 2016

New issue 1233: Add basic sanity checks to ensure yt installation is working after install script finishes https://bitbucket.org/yt_analysis/yt/issues/1233/add-basic-sanity-checks-to… Nathan Goldbaum: See http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2016-June/00792… Responsible: ngoldbaum

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Issue #1232: Absorption Spectrum Error (Gizmo file type)? (yt_analysis/yt)
by Anonymous June 17, 2016

June 17, 2016

New issue 1232: Absorption Spectrum Error (Gizmo file type)? https://bitbucket.org/yt_analysis/yt/issues/1232/absorption-spectrum-error-… Anonymous: I tried using the cookbook code for creating an absorption spectrum (http://yt-project.org/docs/dev/cookbook/cosmological_analysis.html#creating…) for a Gizmo type cosmological simulation file. I created a light ray successfully, create and absorption spectrum via sp = AbsorptionSpectrum(900.0, 1400.0, 50000), and add a HI line to the spectrum, following the cookbook. But whenever I get to the line: wavelength, flux = sp.make_spectrum('lightray.h5', output_file='spectrum.h5', line_list_file='lines.txt', use_peculiar_velocity=True) I get the following error: absorption_spectrum.pyc in _add_lines_to_spectrum(self, field_data, use_peculiar_velocity, output_absorbers_file, subgrid_resolution, observing_redshift, njobs): 444 # edges (ie the wings), then widen the wavelength 445 # window and repeat process. --> 446 if (vtau[0] < min_tau and vtau[-1] < min_tau): 447 break 448 window_width_in_bins *= 2 IndexError: index 0 is out of bounds for axis 0 with size 0 I've looked at the source code but I can't figure out what's causing the problem. If I do not try to add any lines to my absorption spectrum at all, then it doesn't error. But since I'm following the cookbook code, I'm not sure what could be going wrong... Help? Thanks, Kyle Stewart

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