Mailman 3 February 2014 - yt-users

Two Point Correlation Function in yt 3.0 with RAMSES
by David Sullivan 03 Feb '14

03 Feb '14

Hi all, I’m trying to compute the two point halo correlation function for RAMSES data using the code found at http://yt-project.org/docs/2.6/analyzing/analysis_modules/two_point_functio… (I’ve already run HOP and written to HopAnalysis.out). I get an error saying ‘add_tree’ is not defined, but yt.utilities.kdtree is imported and build properly. Is this feature working in version 3.0? Many thanks, David P.S Sorry if this gets duplicated as I accidentally tried to send this with an unregistered e-mail

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Building yt on Hopper
by Andrew Myers 02 Feb '14

02 Feb '14

Hi Folks, I'm trying to install the development version of yt-2.7 on NERSC's Hopper machine using the install script. I get to the part where it tries to build IPython, and then the script fails with the following error message: ============================================================================ BUILDING IPYTHON python: 2.7.6 (default, Jan 31 2014, 21:52:04) [GCC 4.8.1 20130531 (Cray Inc.)] platform: linux2 OPTIONAL DEPENDENCIES sphinx: Not found (required for docs and nbconvert) pygments: Not found (required for docs and nbconvert) nose: 1.3.0 pexpect: no (required for running standalone doctests) Traceback (most recent call last): File "setup.py", line 342, in <module> check_for_dependencies() File "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupbase.py", line 376, in check_for_dependencies check_for_pyzmq() File "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupext/setupext.py", line 118, in check_for_pyzmq import zmq File "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/__init__.py", line 35, in <module> _libzmq = ctypes.CDLL(bundled[0], mode=ctypes.RTLD_GLOBAL) File "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/ctypes/__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) OSError: /global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/libzmq.so: undefined symbol: clock_gettime Both ZeroMQ and pyzmq appear to have been installed without errors, but then ZeroMQ can't find some of the definitions it needs. Googling around, it looks like clock_gettime is supposed to be found in librt. Has anyone seen this before? Or, relatedly, has anyone been able to build yt on the NERSC machines? I know that ZeroMQ isn't strictly necessary, but I'd like to be able to use the notebooks. My complete yt_install.log is here<https://www.dropbox.com/s/pmdq3a9vfrbtwj9/yt_install.log> . Thanks, Andrew

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chemical species abundances discrepancy
by poetaste＠gmail.com 02 Feb '14

02 Feb '14

Hi Guys, I did a simple test with enzo and I tried to plot a radial profile of the chemical species fractions with YT. The problem is that if I use the YT function which intrinsically plot the fraction for a species, let's say H2I_Fraction (as usual), and compare this with a direct evaluation of the mass fraction: data['H2I_Density']/data['Density'] I obtain some slightly different results, mostly at large radii. Anyone might explain this discrepancy!? This happens with all the species. Thank you in advance Stefano

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