Mailman 3 November 2014 - yt-users

Radial Velocity Projection
by John Regan Nov. 25, 2014

Nov. 25, 2014

Hi All, I need to set the "center" field parameter for making a projection of the "radial_velocity". I see from the docs how to do that for a data container but its not clear what to do for a projection. The error I am getting at the moment when the "center" is not set is: File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/data_containers.py", line 249, in __getitem__ self.get_data(f) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/data_containers.py", line 656, in get_data finfo.check_available(self) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/fields/derived_field.py", line 146, in check_available validator(data) File "/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/fields/derived_field.py", line 235, in __call__ raise NeedsParameter(doesnt_have) yt.fields.field_exceptions.NeedsParameter: (['center']) Any tips much appreciated! Cheers, John

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rockstar loading
by Desika Narayanan Nov. 24, 2014

Nov. 24, 2014

Hey All, I'm trying to get started with basic Rockstar halo finding in yt (I typically use HOP, though current analysis requires Rockstar). I'm having trouble with the following line: >from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder which gives the error: http://paste.yt-project.org/show/5224/ I'm running yt 3.0 (updated this morning). I just installed Rockstar (I think) by switching on the INST_ROCKSTAR flag in the install script to 1, and re-running the script. To be sure, I am running in an 'activated' yt, with the following ld_library_path: >(yt-x86_64)thundersnow:~ desika$ echo $LD_LIBRARY_PATH /Users/desika/yt-x86_64/lib:/opt/gsl/lib: Though I note manually adding the directory: /Users/desika/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/ to my ld_library_path doesn't fix the problem. Is this symptomatic of an erroneous installation on my part? thanks -desika

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Fwd: [FLASH-USERS] VisIt 2.7.2 and FLASH 4.2.2
by John ZuHone Nov. 24, 2014

Nov. 24, 2014

Hi yt'ers, Ivo Seitenzahl, a fellow FLASHer and former UChicago colleague, is having trouble with the install script on a HPC system. His issue is copied below. It keeps picking up the Intel compilers, even though he specifies the GNU compiler modules to be loaded. At the moment, I've suggested he set CC=gcc and CXX=g++, but I thought I would copy over here to see if anyone else has any ideas. Best, John > From: Ivo Seitenzahl <ivo.seitenzahl(a)anu.edu.au> > Date: November 23, 2014 at 10:54:09 PM EST > To: John ZuHone <jzuhone(a)space.mit.edu> > Subject: Re: [FLASH-USERS] VisIt 2.7.2 and FLASH 4.2.2 > > Hi John, > so, no luck. I'm trying to do this on raijin. > > http://nci.org.au/nci-systems/national-facility/peak-system/raijin/ > > After logging in, the following modules are loaded. > > [irs120@raijin2 ~]$ module list > Currently Loaded Modulefiles: > 1) pbs 4) openmpi/1.6.3 7) hdf5/1.8.10 > 2) intel-fc/12.1.9.293 5) dot > 3) intel-cc/12.1.9.293 6) szip/2.1 > > So what I've done is 'module unload intel-fc' and 'module unload intel-cc' and 'module load gcc', after which I get > > [irs120@raijin2 ~]$ module list > Currently Loaded Modulefiles: > 1) pbs 2) openmpi/1.6.3 3) dot 4) szip/2.1 5) hdf5/1.8.10 6) gcc/system > > However, for some reason, I still get the same problem (see below). It seems like that icc is still called, instead of gcc, although I only have the gcc module loaded. Any thoughts? > > Thanks, > > Ivo > > >>>>>>>>>>> > > Awesome! Here we go. > > Using wget > Using sha512sum > Setting YT_DIR=/home/120/irs120/yt-x86_64/src/yt-hg/ > Installing distribute > Installing pip > Installing numpy-1.8.2 > Installing matplotlib-1.4.0 > ******************************************** > FAILURE REPORT: > ******************************************** > > extern/qhull/qhull_a.h(106): error: expected a ";" > template <typename T> > ^ > > extern/qhull/qhull_a.h(115): warning #12: parsing restarts here after previous syntax error > void qh_qhull(void); > ^ > > compilation aborted for src/qhull_wrap.c (code 2) > error: command 'icc' failed with exit status 2 > > ******************************************** > ******************************************** > Failure. Check /home/120/irs120/yt-x86_64/yt_install.log. The last 10 lines are

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ds.max_level
by Michael Zingale Nov. 21, 2014

Nov. 21, 2014

If I read in a dataset like: ds = yt.load("ActiveParticleCosmology/DD0046/DD0046") (that file is from the data page) and then do print ds.max_level it gives 99. This happens for the boxlib frontend too. Is there any meaning to the ds.max_level parameter? should we be setting it somewhere? or else remove it? As it is, it is confusing (and tempting to use it) seeing it there. -- 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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yt-2.x: derived fields and field parameters
by Brian O'Shea Nov. 21, 2014

Nov. 21, 2014

Hi yt-users, I am trying to do something that feels like it ought to be simple, but I simply can't figure it out. I am using yt-2.x, and I want to create a derived field based on a given center and a radial profile, which I have pre-calculated and have sent to the derived field using set_field_parameter. This does not seem to work particularly well - I can't seem to get these field parameters, and even my simplest example of a derived field breaks down. Here's a copy of my script: http://paste.yt-project.org/show/5221/ which dies with this traceback: http://paste.yt-project.org/show/5222/ It seems that I can't even access the center that I pass in, much less work with the radial profile. I suspect I'm doing something dumb, but reading the documentation on creating derived fields does not seem to be giving me the clues I need to figure out what I'm doing wrong. Thanks! Brian

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Halo finding on user-given variables
by Adam Jacobs Nov. 21, 2014

Nov. 21, 2014

Hi All, I would like to use yt's halo finder to select out spatially-coherent hotspots in my data. In other words, I would like the halo-finder algorithm to select out based on temperature instead of density. Is this possible? I couldn't find any obvious way to do this in the documentation. Thanks for your assistance! -- Adam Jacobs Department of Physics and Astronomy, PhD Candidate Stony Brook University http://astro.sunysb.edu/amjacobs/

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Confused about units in derived fields
by Jill Naiman Nov. 21, 2014

Nov. 21, 2014

Hi all, As the title states, I am confused - specifically about units. I want to create a derived field where parts of the field are different values, dependent upon some cutoff criteria like so: def _dene2(field,data): tl = data['temperature'] dl = data['density'] print("TEMP") print(tl.in_cgs()) aux = np.where(tl.in_cgs() > 5000.) np.putmask(dl,aux, 0.0) dene = dl return dene ds.add_field("dene", units="g/cm**3", function = _dene2) Not only does this produce a very worrisome error: "RuntimeError: Something has gone terribly wrong, _function is NullFunc for ('flash', 'temp')" The print statement in there shows a bunch of values close to 1, which is why the "aux" mask never returns anything. But why is data a bunch of 1's in here? How do I access/convert to the "real" units? Any help is appreciated, -Jill

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colorbar labels
by Desika Narayanan Nov. 18, 2014

Nov. 18, 2014

Hi All, I have a slice plot that I make with the simple: slc = SlicePlot(pf,'z',('gas','temperature')) slc.zoom(5) slc.save('junk2.png') and produces this (it's super ugly but not the point :) ): http://i.imgur.com/j9H4imp.png I can't figure out how to get the colorbar to reveal the numbers that the colors correspond to. Is there an obvious solution? thanks -d

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Masking the domain?
by Naiman, Jill Nov. 18, 2014

Nov. 18, 2014

Hi all, I'm trying to mask out several spheres in my domain before making a phase plot. Is there a way to do this? I've tried making a derived field, using the boolean mask things, and checked out the "masking domain" section of the cookbook with little success. The regions I want to mask out come from a text file of x/y/z coordinates and radii. Thanks for any insights! -Jill

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Caching and speed
by Mark Krumholz Nov. 17, 2014

Nov. 17, 2014

Hi YT Users, I have a question about speed and caching that I’m hoping someone can help with. I have a fairly large simulation from which I’d like to make projection plots in all three cardinal directions and save the results in a flat numpy array for later incorporation into an animation. One of the quantities I’d like to project is density-weighted temperature, and this is fairly expensive to compute because temperature is a derived field whose construction requires reading 8 other fields from disk. The computation is that temperature = constant times internal energy, and internal energy = total energy (1 field) - magnetic energy (3 fields: Bx, By, and Bz) - kinetic energy (4 fields: density, px, py, pz). I want to do the projection over the entire simulation volume, so it seems like the sensible way to do the computation would be to read all the data once, construct the temperature, store it in memory, and then project it into the three cardinal directions. The size of the data set is not so large that it won’t fit in memory on the largest memory nodes to which I have access. However, what yt seems to be doing instead is to read the data and compute the temperature for the first projection, and then repeat the entire process, including the reading and computation, for each of the other two directions. This makes the computation a factor of 3 slower than it should be (since IO dominates the cost), and, given the size of the data sets involved, this is a significant annoyance. So here’s the question: is there a way to force yt to cache a derived field rather than reconstructing it on the fly every time it is needed? Or is there some other strategy that can be used to avoid this inefficiency? There’s and sample script pasted at https://bpaste.net/show/a58f7ebea9bd <https://bpaste.net/show/a58f7ebea9bd> that demonstrates what I’m trying to do. Thanks. -- Mark Krumholz

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