Mailman 3 May 2013 - yt-dev

yt Strategy Meeting Monday the 22nd
by Matthew Turk Sept. 4, 2013

Sept. 4, 2013

Hi all, I'd like to call a brief, approximately one hour, strategy meeting on Monday, April 22nd at 3PM Eastern. This will cover where yt is at, where we can go, and how things are progressing. Some of this will be dedicated to progress updates (from me and others) as well as soliciting feedback on a number of things. Many other projects -- notably Cactus -- do these on a fixed schedule, so based on the success/failure of this one we can consider having them semi-regularly. The agenda I would like to cover will include: * yt 3.0 status, including near/long term plans for development and support for non-grid codes * Rundown of all YTEPs accepted and outstanding * yt's "presence" on the web * 3.0 paper I will also be soliciting feedback in roundtable style on: * How are we doing? * How is the procedure for code contributions working? * How is the yt "infrastructure" meeting people's needs? (Mailing lists, Bitbucket, etc) * Where are energies being spent that could be better spent elsewhere? If you have either agenda items or discussion items, please reply to this email and suggest them. I think having a large presence at this meeting would be very useful, so if you are able to make it, please try to do so. It'll be held as a google hangout, and I'll send details here when it starts up. If there's a pressing need to reschedule, please write in reply to this email. Thanks, and looking forward to seeing you there, Matt

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NumberDensity in clumps and on FLASH data
by Matthew Turk July 9, 2013

July 9, 2013

Hi all, Mark Richardson wrote to the yt_analysis project with a problem with clumps on FLASH datasets. Here's his email: "Below includes my script and the output (it wouldn't let me attach two files). I get some output in the clump file up until I'd expect to see the Jeans Mass dumped. The output makes me think that it can't calculate this point because Gamma is unknown, or some other essential variable needed to get the number density. I've attempted to change the data_structure.py frontend for Flash to alias Gamma to gamc and game but I still get the 'cannot find Gamma' when loading my dataset." The issue from the traceback is that JeansMassMsun requires MeanMolecularWeight which needs NumberDensity. This can't be generated for his data. I am not an expert on FLASH, but it seems that this should be straightforward to fix, I just don't know how. Anybody from the FLASH or Clump side have any ideas? -Matt

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When can we turn off serialization by default?
by Matthew Turk June 18, 2013

June 18, 2013

Hi all, I'd like to turn off serialization by default. This includes: 1) Projections 2) Grid hierarchy 3) Field lists and maybe other things. In general, I think it's a bad idea to just litter directories with new files, and specifically I think it's a bad idea to store 2&3 since they are a huge source of errors for new and existing users. My preference would be to disable all auto-serialization of anything and make that not possible, mandating explicit, manual saves of data instead. However I recognize that is likely unpopular, as even though my simulations have a lot of data on disk, I know that they also take a relatively short time to project. So when can we make it disabled-by-default? 2.6? 3.0? Now? -Matt

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Issue #582: HaloMassFunction uses Enzo ComovingBoxSize (yt_analysis/yt)
by Matthew Turk May 31, 2013

May 31, 2013

New issue 582: HaloMassFunction uses Enzo ComovingBoxSize https://bitbucket.org/yt_analysis/yt/issue/582/halomassfunction-uses-enzo-c… Matthew Turk: (reported by @mepa ) Inside `yt/analysis_modules/halo_mass_function/halo_mass_function.py` on line 215, there's a reference to `self.pf["ComovingBoxSize"]`. I believe this is then converted into actual Mpc, not Mpc/h, and is then cubed to get the volume of the domain. I am not entirely certain, but I believe this could be replaced either by: `(self.pf.domain_width * self.pf["mpccm"]).prod()` or: `(self.pf.domain_width * self.pf["mpc"]).prod()` depending on whether the mass function is supposed to be proper or comoving; the comments in the code suggest to me very strongly it's the first of the two, not the second. @brittonsmith I am tagging you in the ticket, but if you aren't able to take a look at this feel free to re-assign to me. Responsible: brittonsmith

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Issue #581: Source install error from fKDpy (yt_analysis/yt)
by Casey Stark May 29, 2013

May 29, 2013

New issue 581: Source install error from fKDpy https://bitbucket.org/yt_analysis/yt/issue/581/source-install-error-from-fk… Casey Stark: I'm installing yt-3.0 on NERSC's hopper following the instructions on http://www.nersc.gov/users/software/development-tools/python-tools/. The install fails because the setup script first decides not to build fKDpy.so, but then later tries to copy it to the build directory. Here are the pieces of the log: ``` $ python setup.py install --home=~/python_modules/hopper PNG_LOCATION: png found in: /usr/include, /usr/lib FTYPE_LOCATION: freetype found in: /usr/include, /usr/lib HDF5_LOCATION: HDF5_DIR: /opt/cray/hdf5/1.8.8/gnu/47/include, /opt/cray/hdf5/1.8.8/gnu/47/lib running install running bdist_egg running egg_info running build_src running build_forthon fKDpy.so won't be built due to missing Forthon/gfortran build_src ... running install_data error: can't copy 'yt/utilities/kdtree/fKDpy.so': doesn't exist or not a regular file ``` Am I missing something here?

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Answer test failures
by Nathan Goldbaum May 28, 2013

May 28, 2013

Hi all, It looks like redefinition of the TotalMass field has caused a couple of answer tests to change for the galaxy0030 dataset. See the test reports on Piernik: http://piernik.astri.umk.pl:8080/job/py2.7-yt-2.x_testing/ http://piernik.astri.umk.pl:8080/view/yt-2.x/job/py2.7-yt-2.x_answer.enzo.g… I don't think this is particularly surprising given that the TotalMass field now properly includes star particles. However, given the number of enzo/yt users out there, it might be worthwhile to make a somewhat bigger deal about this change. I'm happy to upload a new set of answer test results and issue a pull request for the update. I'll try to get that done tonight. -Nathan

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Issue #580: In LightRay, halo list is missing "center" when getting straight from halo profiler. (yt_analysis/yt)
by Britton Smith May 26, 2013

May 26, 2013

New issue 580: In LightRay, halo list is missing "center" when getting straight from halo profiler. https://bitbucket.org/yt_analysis/yt/issue/580/in-lightray-halo-list-is-mis… Britton Smith: When loading the halo list straight from the halo profiler in the light ray tool, it appears to be missing the halo centers. The error looks like this: Traceback (most recent call last): File "../analysis/make_light_ray_0.1_Lstar.py", line 120, in <module> njobs=-1) File "/nics/a/proj/cosmo/local-britton/nautilus/src/yt-britton/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", line 409, in make_light_ray **halo_profiler_parameters) File "/nics/a/proj/cosmo/local-britton/nautilus/src/yt-britton/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", line 469, in _get_halo_list halo_list=halo_list) File "/nics/a/proj/cosmo/local-britton/nautilus/src/yt-britton/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", line 502, in _halo_profiler_list return_list[field].append(halo[field]) KeyError: 'center' Responsible: brittonsmith

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Issue #579: Plot window modifying functions need to be documented better. (yt_analysis/yt)
by Nathan Goldbaum May 24, 2013

May 24, 2013

New issue 579: Plot window modifying functions need to be documented better. https://bitbucket.org/yt_analysis/yt/issue/579/plot-window-modifying-functi… Nathan Goldbaum: We should add narrative docs for the plot window modifying functions (e.g. `set_zlim`, `set_log`, `zoom`, `pan`) to the page that covers the plot callbacks. Since `PlotCollection` is still usable but deprecated for image plotting, we could also give the full names for the callbacks (`annotate_<callback>`) rather than the shortened name. Responsible: ngoldbaum

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Reminder: 2.5.3 and 3.0a2 releases next week
by Matthew Turk May 24, 2013

May 24, 2013

Hi all, Just a reminder that next Saturday we're scheduled to put out bugfix for 2.X, which will be 2.5.3, and a second alpha of yt 3.0. I'll probably roll these up either Friday night or the following Monday morning. So if you have any changes you'd like to get in, let's aim to have them PR'd by Wednesday or so, and I think we should freeze non-critical fixes after that. 2.5.3 will have a number of minor improvements, but I think we'll probably wait until after it goes out to merge in the Boxlib consolidation, even if that gets finished. The 3.0 alpha will include a ton of improvements to Octree stuff, as well as preliminary particle deposition. This means Tipsy & Gadget will have the most basic of support. RAMSES has had a number of improvements to its IO and units. For the third alpha (July 15) I'd like to target units, the "global mesh" issue, and perhaps SPH smoothing kernels. -Matt

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Issue #578: HaloProfiler runs out of ram on large datasets. (yt_analysis/yt)
by Britton Smith May 24, 2013

May 24, 2013

New issue 578: HaloProfiler runs out of ram on large datasets. https://bitbucket.org/yt_analysis/yt/issue/578/haloprofiler-runs-out-of-ram… Britton Smith: The HaloProfiler will often eventually run out of memory while profiling large datasets with many halos. There are calls to clear data after each profile is made, but these don't seem to help. Responsible: brittonsmith

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