Mailman 3 April 2014 - yt-dev

Vorticity
by Matthew Turk 15 Apr '14

15 Apr '14

Hi all, I have been working with Jia-Hung on looking at vorticity in his GAMER simulations. He has supplied me with a dataset where the minimum vorticity (by prescription) should be at the center. After a lot of back and forth with him and with Jeff Oishi, I determined that what looks to be happening is that unless I set the number of ghost zones to 2 (instead of 1) there is a systematic offset. Can anybody think why this might be? I'm working on making this into a unit test to check its behavior in 3.0. -Matt

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Issue #829: 'unitary' no longer works properly (yt_analysis/yt)
by Kacper Kowalik 15 Apr '14

15 Apr '14

New issue 829: 'unitary' no longer works properly https://bitbucket.org/yt_analysis/yt/issue/829/unitary-no-longer-works-prop… Kacper Kowalik: With revision eaf23ee following code: ``` #!python from yt.mods import load pf = load('DD0010/moving7_0010') sp = pf.h.sphere('max', (0.1, 'unitary')) ``` yields: ``` #!text Traceback (most recent call last): File "/tmp/ala.py", line 6, in <module> sp = pf.h.sphere('max', (0.1, 'unitary')) File "/tmp/yt/yt/data_objects/selection_data_containers.py", line 562, in __init__ self.index.get_smallest_dx().in_units("code_length")) yt.utilities.exceptions.YTSphereTooSmall: 1.78097e-25 < 4.88281e-04 ``` Responsible: ngoldbaum

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standard for code meta data
by Michael Zingale 14 Apr '14

14 Apr '14

I'm playing around with the Maestro/BoxLib frontend. Maestro (and Castro) plotfiles contain a file called job_info that stores a lot of metadata, including the values of all runtime parameters and the git hashes corresponding to which versions of the various codes were used to build the executable. Currently we have all of the runtime parameters stored in the parameters dictionary. I'd like to add the version control hashes in a dictionary as well. I can add them to the same parameters file, but I am wondering if other codes use a standard place for this. Ultimately I'd like to save some of this information (especially the code hashes) in the output files that yt generates: i.e. as png metadata, simple postscript comments for eps files, or pdf metadata for pdf files. This will help complete the link toward reproducibility in that it will preserve the chain of information from code to output to plot. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

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Defining new particle unions?
by Nathan Goldbaum 12 Apr '14

12 Apr '14

Hi all, I'm trying to define a particle union for my dataset that represents stars formed during the simulation. The most straightforward way to accomplish this is to use a mass cut. Does anyone have examples of how to set up a particle union? Bonus if it uses enzo data. In return for any helpful advice anyone can give, I will add sorely needed documentation for particle unions to the 3.0 docs. -Nathan

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Hub and AWS downtime
by Matthew Turk 12 Apr '14

12 Apr '14

Hi all, The yt data hub and affiliated services are going to go down for a little while; I hope this will be less than a few days, but we need to migrate off of the AWS services over to Rackspace. This will include storage of answer testing (both yt and Enzo) as well as the hub. I am leaving the blog up for the time being, but it will need to migrate as well eventually. Again, I am aiming to have a short downtime... but it might be up to a week. -Matt

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Tipsy _is_valid will deadlock loading FLASH datasets
by Nathan Goldbaum 11 Apr '14

11 Apr '14

Hi all, We just had a bug report from Aaron Smith at UT Austin. The symptom is that the "load" comman was taking 30 seconds to complete on his FLASH dataset, which should never happen for FLASH. After asking him to profile the code, he produced the following profile: http://ngoldbaum.net/yt-load/ It seems that the recent changes to the Tipsy frontend which allow it to autodetect binary outputs have made it so in some cases non-tipsy data is loaded off disk. I'm not sure about the best way to handle this, which is why I'm writing to the list rather than issuing a PR. -Nathan

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sorted particle indices when loading halos from disk
by Josh Moloney 09 Apr '14

09 Apr '14

Recently I've been working with the HOP halo finder in yt 3.0. In particular I've been looking at star particles from Enzo simulations in halos of different sizes. I've been running into strange results with particle fields that are stored in the halo hdf5 files vs particle fields that have to be retrieved from the original simulation data. In particular, if I create a mask for star particles from a field saved to disk (creation_time prior to 3.0 or ParticleMassMsun now) then I get the correct values for other fields when I use this mask if they were also saved to disk (so particle positions or velocities) but not for fields that were retrieved from the simulation (such as dynamical time). Similarly, if I identify stars by creation_time in 3.0 (when it isn't saved in the hdf5 file) then I get the correct dynamical_times, but incorrect particle masses. I think I've identified the source of this problem. When the "particle_index" field is read from the halo hdf5 files, it is then sorted into ascending order. In particular, in __getitem__ in the LoadedHalo class there is the following (this is line ~867 in halo_objects in the 3.0 experimental branch): field_data = self._get_particle_data(self.id, self.fnames, self.size, key) if field_data is not None: if key == 'particle_index': field_data = field_data[field_data.argsort()] These sorted particle indices are then used when retrieving fields from the simulation data, so the fields end up being sorted in a different order than the ones that are retrieved directly from the halo hdf5 files. As a result, masks created from one set of fields don't work properly on the other set. I think that I can fix this, but before I do I want to make sure I'm not going to be breaking anything else in the process. Does anyone know why the particle_index field was being sorted? If so, do you happen to know whether it would make more sense to sort the other particle fields from disk or leave particle_index unsorted? Thanks in advance for any help. - Josh

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Heads up if you use bitbucket over HTTPS
by Nathan Goldbaum 09 Apr '14

09 Apr '14

Due to the recently revealed "heartbleed" OpenSSL bug bitbucket will be updating their SSL certificate. If you talk to bitbucket over HTTPS (ssh is unaffected) you might start seeing some error messages. See this blog post for more information: http://blog.bitbucket.org/2014/04/08/bitbuckets-ssl-certificates-are-changi… Hope that's helpful, Nathan

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Species fields
by Matthew Turk 07 Apr '14

07 Apr '14

Hi all, There've been three big pushes on adding species fields in a generic way to yt recently. * Enzo * OWLS * FIRE Britton came up with an idea that I think works quite nicely. The field info container is responsible for enumerating a list of species that it finds, on startup. Then, when the field plugins are added, the field plugin looks for all of the fields that it can find that are related to each species enumerated, and the appropriate fraction/density/number density fields get added. Right now, the field plugin is not created yet, but that is my next step for this. What the plugin will do is iterate over all the species names, try to find the appropriate fields in the pf.field_aliases, and then appropriately add things. What this means is that if the frontend, in setup_fluid_fields, ensures that the species names are all appended to the species_list, the plugin will then create all of the appropriate fields. So if it finds "He_p1" in the species_list, it will look to see if "He_p1_fraction" exists, then look for _density, and _number_density, and whichever one it finds it will use to create derived fields for the others. Where this gets a bit messy is in the actual creation of all of the aliases, which is why I think it's appropriate for it to be a plugin. Once we have these aliases, we can add on smoothed versions of the fields. By basing this on a recognized list of species types, we can also reduce the number of fields looked for by the plugin system to just those it knows it ought to make. And, since we have "species" objects, we can create those on-demand to use. Gabe did some work with this for the OWLS datasets, where he created all of the ionization states based on the density fields. What I'm suggesting here is that with this plugin, he could create *just* the ionization states in density or fraction form, and then the plugin would create the alternates *and* all the smoothed fields. This does open up the question of what to do about *neutral* species, as distinct from *total nuclei*, which the natural representation of is somewhat degenerate. Britton opted for a %s_nuclei_%s naming scheme, where Gabe opted to specify Symbol_%s, with explicit p0 suffices for those neutral fractions. Originally, I wanted _p0, and I think I still do, but I recognize not everyone agrees. The other item Gabe worked on, which I promised I'd write up into a YTEP, was changing the particle deposition types. This will be a forthcoming email, out of scope for this one. Any feedback from anyone? I intend to consolidate all of the detection shortly and make it into a plugin, but I'll need help, especially from Gabe on the OWLS part of this. -Matt

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paste.yt-project.org down?
by Nathan Goldbaum 07 Apr '14

07 Apr '14

Hi all, It looks like paste.yt-project.org is down - all I'm seeing right now at that URL is a directory listing including two favicons and an error message. -Nathan

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