Mailman 3 May 2011 - yt-users

Re: [yt-users] Problem with common unstable branch on Kraken
by Anthony Harness May 26, 2011

May 26, 2011

Britton, Adding those lines works for the stable install, which I guess is maintained by Hari. My problem was running the unstable install maintained by Stephen, which he informed me does not work in parallel. As Stephen mentioned before, if Hari could update his development install, I could use that instead. Thanks, Anthony

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Problem with common unstable branch on Kraken
by Anthony Harness May 26, 2011

May 26, 2011

Using the "unstable" version of yt on Kraken, I get the following error while simply trying to import yt while running in parallel. I haven't done anything memory-intensive, so I suspect this is a bug. I have the PrgEnv-gnu module loaded. Traceback (most recent call last): File "/lustre/scratch/harnessa/analysis/Clumping/test2.py", line 1, in <module> from yt.mods import * File "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/yt-2.2dev-py2.7-linux-x86_64.egg/… [View More]

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yt update problem (ramses?)
by Molly Peeples May 25, 2011

May 25, 2011

Hi, I just tried updating to the latest version of yt [173a08b2e892 (yt) tip] on triton, but I'm getting: cythonc:> build/src.linux-x86_64-2.6/yt/frontends/ramses/_ramses_reader.cpp Error converting Pyrex file to C: ------------------------------------------------------------ ... tr[0,i] = self.left_edge[i] tr[1,i] = self.right_edge[i] tr[2,i] = self.dimensions[i] return tr @cython.cdivision ^ -----------------------------------------------------… [View More]

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possible bugs in analytical mass function code and halo profiler code
by Michael Kuhlen May 24, 2011

May 24, 2011

I think I've identified a bug in the analytical mass function code, and a possible bug or improvement in the halo profiling code: 1) In yt/analysis_modules/halo_mass_function/halo_mass_function.py line 327, shouldn't dn_M_z be multiplied by h^3 instead of h^4? 2) In yt/analysis_modules/halo_profiler/halo_filters.py, I've found that the way the virial radius is determined often doesn't work very well for me. a) I commonly find that more than the first few bins in the profile … [View More] have overDensity <= virial_overdensity, even though there's nothing wrong with the halo profile. It's just a transient, perhaps caused by too small bin sizes. Just a little bit farther from the center the profile becomes reasonable again, with overDensity > virial_overdensity and decreasing outwards. In these cases, this condition (line 100) if (overDensity[1] <= virial_overdensity): index = 0 results in this halo getting an incorrect virial radius and getting tossed out as "not virialized". b) Related to the previous point, I've found that determining the virial radius (the bin where overDensity drops below virial_overdensity) from the inside-out, as in (line 105) for q in (na.arange(len(overDensity)-2))+2: if (overDensity[q] < virial_overdensity): index = q - 1 break doesn't work as well as an outside-in approach. I've gotten much better results, i.e. fewer rejected halos that were perfectly fine and better virial radii, by doing this: if (overDensity[-1] >= virial_overdensity): index = -2 else: for q in (na.arange(len(overDensity),0,-1)-1): if (overDensity[q] < virial_overdensity) and (overDensity[q-1] > virial_overdensity): index = q - 1 break 3) Lastly, one question about the radial profiles. I've noticed that the 'CellVolume' field is rarely equal to 4.0/3.0 * pi * ('RadiusMpc' * 3.09e24)**3. Typically 'CellVolume' is about 35 - 40% larger. Maybe this is because the grid cells partly "overshoot" the edge of the sphere? But I'm surprised that this is a 35% effect... This potentially affects the determination of the virial radius. Thanks, Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 601 Campbell Hall * * skype username: mikekuhlen Berkeley, CA 94720 * * * ********************************************************************* [View Less]

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error in the field SoundSpeed?
by luigi＠ita.uni-heidelberg.de May 24, 2011

May 24, 2011

Dear all, I want to point out that, in the unstable branch, any attempt of using the field SoundSpeed returns an error. I have the impression that yt looks for GasEnergy, but in my dataset I have Gas_Energy defined. In the stable branch everything works well. I hope it does not depend on the data I'm analysing (some old Enzo 1.0 output)... Cheers, Luigi --------------------------------------------------------------- Luigi Iapichino Zentrum fuer Astronomie der Universitaet … [View More]

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Problem with Derived Quantities/Fields while running in parallel
by Anthony Harness May 24, 2011

May 24, 2011

I am running yt-2.1stable with python2.7 on Kraken and run into this problem: When I call a derived quantity that calls a derived field that calls a universal field, I get an error: "AttributeError: 'fake_parameter_file' object has no attribute 'parameters'" which arises in the universal field's convert function in 'data_objects/universal_fields.py' With the following code: #derived Field def _test2(field,data): return data['Baryon_Overdensity'] add_field('test2',function=_test2,… [View More]

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Mecurial compilation error
by Stella Offner May 23, 2011

May 23, 2011

Hi, I'm attempting to install a new version of yt on the Harvard Odyssey machine (dual Xeon quad core). The install fails when building mecurial. Does anyone recognize this error? ... running build_ext building 'mercurial.base85' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/mercurial gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/n/sw/python-2.7/include/python2.7 -c mercurial/base85.c -o build/temp.… [View More]

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define a general derived field from other fields
by gso＠physics.ucsd.edu May 19, 2011

May 19, 2011

Hi all, I'm currently trying to find a way to define a clumping factor by giving this formula (for unigrid simulation no AMR): def _HIIClumpingFactorParts(data): square_HIIdensity = (data["HII_Density"]**2).sum() sum_HIIdensity = (data["HII_Density"]).sum() return square_HIIdensity, sum_HIIdensity def _HIIMultiplyParts(data, square_HIIdensity, sum_HIIdensity): return data.quantities["TotalQuantity"]("Ones")[0]*square_HIIdensity.sum()/sum_HIIdensity.sum()**2 add_quantity("… [View More]

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question on the halo profiler
by Luigi Iapichino May 19, 2011

May 19, 2011

Dear all, I have the following (rather standard, I guess) problem: I want to produce radial profiles of selected quantities, from a number of halos in my cosmological box. I am using the yt halo profiler, in the unstable branch. So far, I am able to add filters in such a way to select as many halos as I want, but I have problems with setting the outer radius of my profiles. Here are the relevant parts of my script: ... import yt.analysis_modules.halo_profiler.api as HP ... hp = HP.… [View More]

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installing yt on mac OS bzlib issue
by Jean-Claude Passy May 18, 2011

May 18, 2011

Hi all, I am able to install yt on my Mac if I turn off the Bzlib option. When it is turned on, the installation fails the following way: ----------------------------------------------------------------------------------------------------------------------------- echo ".so man1/bzgrep.1" > /Users/jean-claudepassy/Work/yt-i386/man/man1/bzegrep.1 echo ".so man1/bzgrep.1" > /Users/jean-claudepassy/Work/yt-i386/man/man1/bzfgrep.1 echo ".so man1/bzmore.1" > /Users/jean-claudepassy/… [View More]

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