Mailman 3 May 2011 - yt-users

Re: [yt-users] Problem with common unstable branch on Kraken
by Anthony Harness 26 May '11

26 May '11

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 26 May '11

26 May '11

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/yt/mods.py", line 35, in <module> import numpy as na # For historical reasons File "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/numpy/__init__.py", line 154, in <module> import ctypeslib File "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/numpy/ctypeslib.py", line 60, in <module> import ctypes File "/lustre/scratch/proj/yt_common/unstable/lib/python2.7/ctypes/__init__.py", line 549, in <module> CFUNCTYPE(c_int)(lambda: None) MemoryError Thanks, Anthony

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yt update problem (ramses?)
by Molly Peeples 25 May '11

25 May '11

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 ^ ------------------------------------------------------------ /home/molly-ucla/yt-x86_64/src/yt-hg/yt/frontends/ramses/_ramses_reader.pyx:865:0: Cdef functions cannot take arbitrary decorators. error: 1 errors while compiling 'yt/frontends/ramses/_ramses_reader.pyx' with Cython Any ideas what I need to do? Thanks, --Molly

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possible bugs in analytical mass function code and halo profiler code
by Michael Kuhlen 24 May '11

24 May '11

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 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 * * * *********************************************************************

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error in the field SoundSpeed?
by luigi＠ita.uni-heidelberg.de 24 May '11

24 May '11

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 Heidelberg Institut fuer Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail: luigi(a)ita.uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/

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Problem with Derived Quantities/Fields while running in parallel
by Anthony Harness 24 May '11

24 May '11

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,units=r"") #derived quantity def _test(data): return data['test2'] def _combTest(data,arr): return arr.sum() add_quantity('test',function=_test,combine_function=_combTest,n_ret=1) dd.quantities['test']() I get the error: AttributeError: 'fake_parameter_file' object has no attribute 'parameters' from line 418, in _Convert_Baryon_Overdensity in universal_fields.py: "data.pf.parameters.has_key('omega_baryon_now'):" So it seems as if the parameter file is not being passed from the derived quantitty all the way to the universal field. This works fine when I run it in serial, but fails when it is ran in parallel. Any suggestions? Thanks

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Mecurial compilation error
by Stella Offner 23 May '11

23 May '11

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.linux-x86_64-2.7/mercurial/base85.o gcc -pthread -shared -L/n/home05/soffner/yt-x86_64/lib/ -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/ -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/ -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/ -L/n/home05/soffner/yt-x86_64/lib64/ build/temp.linux-x86_64-2.7/mercurial/base85.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/mercurial/base85.so /usr/bin/ld: /n/home05/soffner/yt-x86_64/lib//libpython2.7.a(exceptions.o): relocation R_X86_64_32 against `_Py_NoneStruct' can not be used when making a shared object; recompile with -fPIC /n/home05/soffner/yt-x86_64/lib//libpython2.7.a: could not read symbols: Bad value collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1 Python 2.7 seems to work ok, so I don't know what the deal is with the libpython2.7a error. Thanks, Stella

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define a general derived field from other fields
by gso＠physics.ucsd.edu 19 May '11

19 May '11

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("HIIClumpingFactor", function=_HIIClumpingFactorParts, combine_function=_HIIMultiplyParts, n_ret = 2) I was wondering how I can generalize this formula to be used with different fields if I want to say get the clumping factor of HI_Density, or HeI_Density, Dark_Matter_Density etc? From G.S.

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question on the halo profiler
by Luigi Iapichino 19 May '11

19 May '11

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.HaloProfiler(data_dir, halos="multiple",halo_radius=500,radius_units="kpc",n_profile_bins=20) ... In particular, I am not able to change the outer radius by setting halo_radius. I read in the manual: " halo_radius (float): if no halo radii are provided in the halo list file, this parameter ..." etc. Now, in the halo list file provided by the HOP tool (within yt) there is an entry called max_r. Is it a problem if I want to override it and set the outer radius differently? As a side note, however max_r is >not< the current outer radius that I found in my in Halo_0000_profile.dat . I look forward to your suggestions, Cheers, Luigi -- --------------------------------------------------------------- Luigi Iapichino Zentrum fuer Astronomie der Universitaet Heidelberg Institut fuer Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail: luigi(a)ita.uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/

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installing yt on mac OS bzlib issue
by Jean-Claude Passy 18 May '11

18 May '11

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/Work/yt-i386/man/man1/bzless.1 echo ".so man1/bzdiff.1" > /Users/jean-claudepassy/Work/yt-i386/man/man1/bzcmp.1 gcc -shared -Wl,-install_name -Wl,libbz2.so.1.0 -o libbz2.so.1.0.4 blocksort.o huffman.o crct\ able.o randtable.o compress.o decompress.o bzlib.o Undefined symbols: "_main", referenced from: start in crt1.10.5.o ld: symbol(s) not found collect2: ld returned 1 exit status make: *** [all] Error 1 ----------------------------------------------------------------------------------------------------------------------------- Does anyone have an idea how to fix this ? Thanks a lot, JC

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