Mailman 3 September 2013 - yt-users

error installing mecurial during yt install
by Brendan Griffen 04 Sep '13

04 Sep '13

Hi, I am doing a fresh install so I downloaded the install_script.sh and did the usual bash install_script.sh I got this error though: .... INST_ZLIB = 1 so I will be installing zlib INST_BZLIB = 1 so I will be installing bzlib INST_PNG = 1 so I will be installing libpng INST_FTYPE = 1 so I will be installing freetype2 INST_SQLITE3 = 1 so I will be installing SQLite3 INST_HG = 1 so I will be installing Mercurial INST_ENZO = 0 so I won't be checking out Enzo INST_PYX = 0 so I won't be installing PyX INST_SCIPY = 1 so I will be installing scipy INST_0MQ = 1 so I will be installing ZeroMQ INST_ROCKSTAR = 1 so I will be installing Rockstar .... Downloading xray_emissivity.h5 from yt-project.org Installing mercurial-2.7 ******************************************** FAILURE REPORT: ******************************************** running build running build_mo running build_ext building 'mercurial.base85' extension gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/n/sw/python-2.7.1/include/python2.7 -c mercurial/base85.c -o build/temp.linux-x86_64-2.7/mercurial/base85.o gcc -pthread -shared -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib64/ -L/n/home01/bgriffen/data/lib/yt-x86_64/lib/ -L/n/home01/bgriffen/data/lib/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/home01/bgriffen/data/lib/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/home01/bgriffen/data/lib/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 ******************************************** ******************************************** Can anyone suggest a work-around? Thanks. The cluster I'm on also has mecurial installed and I can load that module if needs be. I'm not sure if it is critical to getting yt working. Thanks. Brendan

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SlicePlot script stuck
by Jean-Claude Passy 04 Sep '13

04 Sep '13

Hi all, I am running a simple script using SlicePlot (see attached) on a small dataset (only ~ 200k cells). While it works without any problem on my laptop OS X 10.8.4, it gets stuck after saving the first slice (see below) on a remote Linux machine. I have run the script on the same data on both machines, have installed the latest dev version of yt, even removed the *.yt files. But it did not help. Does anyone have a suggestion? Thanks a lot, JC ------------------------------------------------------------------------------------------------------------------------------------------------- [ 7:48:12] seawolf2:$ python2.7 ~/Enzo/python/PlotEnzoDataMultiple.py 0 0 1.0 yt : [INFO ] 2013-09-03 07:48:34,165 Parameters: current_time = 0 yt : [INFO ] 2013-09-03 07:48:34,165 Parameters: domain_dimensions = [32 32 32] yt : [INFO ] 2013-09-03 07:48:34,166 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2013-09-03 07:48:34,167 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2013-09-03 07:48:34,168 Parameters: cosmological_simulation = 0.0 loading DD0000/CE0000 yt : [INFO ] 2013-09-03 07:48:34,174 Getting the binary hierarchy Parsing Hierarchy100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [INFO ] 2013-09-03 07:48:34,181 Gathering a field list (this may take a moment.) yt : [INFO ] 2013-09-03 07:48:34,220 Adding unknown field Grav_Potential to list of fields level # grids # cells # cells^3 ---------------------------------------------- 0 1 32768 31 1 1 13824 23 2 6 56320 38 3 14 85936 44 ---------------------------------------------- 22 188848 t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years Smallest Cell: Width: 4.431e-14 Mpc Width: 4.431e-14 mpc Width: 4.431e-11 kpc Width: 4.431e-08 pc Width: 3.906e-03 1 Width: 3.906e-03 aye Width: 3.906e-03 unitary Width: 9.139e-03 au Width: 1.966e+00 rsun Width: 8.495e+05 miles Width: 1.367e+06 km Width: 1.367e+11 cm yt : [INFO ] 2013-09-03 07:48:34,600 xlim = 0.000000 1.000000 yt : [INFO ] 2013-09-03 07:48:34,600 ylim = 0.000000 1.000000 yt : [INFO ] 2013-09-03 07:48:34,600 Making a fixed resolution buffer of (Density) 800 by 800 yt : [INFO ] 2013-09-03 07:48:34,610 xlim = 0.000000 1.000000 yt : [INFO ] 2013-09-03 07:48:34,610 ylim = 0.000000 1.000000 yt : [INFO ] 2013-09-03 07:48:34,610 Making a fixed resolution buffer of (Density) 800 by 800 yt : [INFO ] 2013-09-03 07:48:34,619 Making a fixed resolution buffer of (Density) 800 by 800 yt : [INFO ] 2013-09-03 07:48:35,467 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,471 Getting particle_position_z using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,669 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,674 Getting particle_position_z using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,681 Making a fixed resolution buffer of (Density) 800 by 800 yt : [INFO ] 2013-09-03 07:48:35,881 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,885 Getting particle_position_z using ParticleIO yt : [INFO ] 2013-09-03 07:48:35,892 Making a fixed resolution buffer of (Density) 800 by 800 yt : [INFO ] 2013-09-03 07:48:36,091 Getting particle_position_y using ParticleIO yt : [INFO ] 2013-09-03 07:48:36,095 Getting particle_position_z using ParticleIO yt : [INFO ] 2013-09-03 07:48:36,102 Saving plot Plots/Density/x-axis/CE0000_Slice_x_Density.png -------------------------------------------------------------------------------------------------------------------------------------------------

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yt unable to find sip module
by Gary Foreman 03 Sep '13

03 Sep '13

Hello, Suddenly my yt distribution seems to be broken because it cannot find the module sip. Sip appears to be a python/C interface that is called by matplotlib.pyplot. I have tried a few things to resolve the issue, none of which have worked. I've tried: yt update --all, pip install sip, and apt-get install yt using the repository mentioned on the Get YT page. pip install and apt-get install fail for separate reasons, which I can explain in a future email if necessary. Since first encountering this problem, I have updated my OS because I realized I was using an outdated version of Ubuntu. I am now running Ubuntu 12.4 LTS. The OS update did not resolve the issue. It seems worth mentioning that the default system python distribution is working fine and I am able to import pyplot as well as sip without a problem. During a quick search of the yt distribution, I did not find the same sip related files that I have in my system's python distribution. Also, as of Friday, things are working fine with the yt distribution I have on my Mac laptop. Thanks very much in advance for your help. Please let me know if you would like me to post some of the error messages I have received from the few solutions that I've tried. Gary

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