Mailman 3 May 2012 - yt-users

Installation failure
by Chao Shi 27 May '12

27 May '12

Hi again, Just a moment ago I sent an email asking help for readline service. After that I deleted and tried to re-re-install yt again. But this time I got these errors: adding yt/visualization/volume_rendering/transfer_functions.py revisions files: 1636/1637 chunks (99.94%) adding yt_unstable.kpf revisions files: 1637/1637 chunks (100.00%) added 5570 changesets with 13259 changes to 1637 files (+2 heads) sending listkeys command updating the branch cache abort: HTTP Error 502: Bad Gateway abort: repository /home/cshi31/yt-x86_64/src/yt-hg/ not found! /home/cshi31/yt-x86_64/bin/python2.7: can't open file '/home/cshi31/yt-x86_64/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory I'm still using the automatic way to install. It seems that the server is down temporarily? Thanks, Chao

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Over plot particles
by REMUDIN RESHID MEKURIA 24 May '12

24 May '12

Dear all, Thank you for your help in advance. I am currently running cosmological simulations using Nyx code. And while trying to over plotting particles on the density slice, I encountered the following error which I couldn't resolve. I will greatly appreciate your help. Traceback (most recent call last): File "./OverPlotingParticles.py", line 14, in <module> pc.set_width(1.0, '1') # change width of our plot to the full domain File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 267, in set_width plot.set_width(width, unit) File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 441, in set_width self._refresh_display_width() File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 459, in _refresh_display_width self._redraw_image() File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 406, in _redraw_image self._run_callbacks() File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 259, in _run_callbacks cb(self) File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 985, in __call__ & ( reg[field_y] >= y0 ) & ( reg[field_y] <= y1 ) ) File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 319, in __getitem__ self.get_data(key) File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 2410, in get_data if self._generate_field(field): File "/home/uni06/cosmo/rmekuri/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 352, in _generate_field raise KeyError(field) KeyError: 'particle_position_y' With best regards, Cheers, Remudin ------ Remudin Reshid Mekuria phone: +49 (0)551 39-13805 IAG, Friedrich-Hund-Plaz 1 fax: +49 (0)551 39-5043 D-37077 Goettingen Germany

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YTSphereTooSmall
by Geoffrey So 23 May '12

23 May '12

I get this behavior when I was trying to compare the sphere stuff with my ellipsoid mod, I sometimes get spheres that are bigger than the cell yet raise the exception YTSphereTooSmall. In my script I print out the sphere's radius, virial radius (halo.maximum_radius(), halo.virial_radius()) and halo number (halo.id), and prints out a smaller than cell warning and return 0 for all attributes when it raises the YTSphereTooSmall exception: halo 5 radius 1.5050650880000000e-02 virial radius 1.2055938905417463e-03 smaller than cell on core 5 halo 4 has max radius 1.2223814100000001e-02 virial radius 5.3953301266098522e-03 halo 2 has max radius 1.9527046860000001e-02 virial radius 4.1620297341626667e-03 halo 3 has max radius 1.0534633139999999e-02 virial radius 5.3662327185065445e-03 halo 1 has max radius 1.8385822579999999e-02 virial radius 4.6616257644500492e-03 halo 0 has max radius 2.7329332320000000e-02 virial radius 6.9309345140911253e-03 Since this is a unigrid run with no AMR, the check in data_objects.py should be the same self.hierarchy.get_smallest_dx() if radius < self.hierarchy.get_smallest_dx(): raise YTSphereTooSmall(pf, radius, self.hierarchy.get_smallest_dx()) The resolution is 800 cube so 1/800 dx should be 1.25e-03. The only thing smaller than 1.25e-03 is the virial radius of halo 5, but the halo sphere object was obtained using halo.get_sphere() which according to the Doc page uses the maximum_radius() by default. So it looks like the sphere has a radius from maximum_radius(), but during the check to see if "radius" is too small, it is using the virial radius instead. Is this something intended? From G.S.

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error while installing yt on Mac OSX Lion
by Jun-Hwan Choi 22 May '12

22 May '12

Hi yt users, I try to install yt in Mac OS lion and encounter failure. The yt_install.log shows following message at the end of log: ....... running install_egg_info Writing /Users/jhchoi/common/lib/python2.7/lib-dynload/Python-2.7.2-py2.7.egg-info if test -f /Users/jhchoi/common/bin/python -o -h /Users/jhchoi/common/bin/python; \ then rm -f /Users/jhchoi/common/bin/python; \ else true; \ fi (cd /Users/jhchoi/common/bin; ln python2.7 python) rm -f /Users/jhchoi/common/bin/python-config (cd /Users/jhchoi/common/bin; ln -s python2.7-config python-config) test -d /Users/jhchoi/common/lib/pkgconfig || /usr/bin/install -c -d -m 755 /Users/jhchoi/common/lib/pkgconfig rm -f /Users/jhchoi/common/lib/pkgconfig/python.pc (cd /Users/jhchoi/common/lib/pkgconfig; ln -s python-2.7.pc python.pc) /usr/bin/install -c -m 644 ./Misc/python.man \ /Users/jhchoi/common/share/man/man1/python2.7.1 Traceback (most recent call last): File "setup.py", line 418, in <module> version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0].splitlines()[0] IndexError: list index out of range I use the most updated install_script.sh from yt web page. F.Y.I. I install gcc and g++ through Xcode(xcode_432_lion.dmg) w/ command line tools (cltools_lion_latemarch12.dmg). Thanks in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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yt users survey, Spring 2012
by matthewturk＠gmail.com 21 May '12

21 May '12

If you have trouble viewing or submitting this form, you can fill it out online: https://docs.google.com/spreadsheet/viewform?formkey=dEtHNXFXbXZJTXZUQ3dWaU… yt users survey, Spring 2012 It's that time of year again! We'd like some feedback on your use and your opinions about the present and future of yt. It's really short, and no questions are mandatory, so feel free to fill in as many or as few as you'd like. Do you find that yt is: Easy to use Difficult to use Too hard to use How often do you use yt? All the time Once in a while I tried, and it broke, so I stopped Have you used the yt GUI, Reason? Yes, often Yes, once or twice No Never heard of it The thing I think yt needs, more than anything else is ... More supported codes Speed or parallelism improvements More canned tasks for astrophysical analysis Better/easier visualization not destined for publication Better/easier visualization for publication Improvements to the GUI API documentation Narrative documentation and tutorials A more friendly development process or community More reliability or error handling Ability to conduct time series analysis Other: Anything to add about deficiencies in yt? What should be changed about the documentation? There's too much -- slim it down! I want more narrative documentation I want more example scripts The organization should be improved I'd like more screencasts Other: Have you watched the yt workshop videos? I was not there and did not watch any videos I was not there and did watch one or more videos I was there and did not watch any videos I was there and did watch one or more videos Which of these pieces of functionality have you used: yt pastebin (the yt pastebin) Clump finder Halo finder Volume renderer IRC for yt help Time series analysis Volume rendering in yt is ... Attractive Hard to get right Slow Easy to set up Have you found anything in yt to be particularly annoying? How do you find the yt community to be? Have you ever contributed code to yt? If so, what was good or bad about that experience? If there's one message about yt you want to send, what is it? If you want to be contacted about anything you've written, put your contact info here. Powered by Google Docs Report Abuse - Terms of Service - Additional Terms

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error while installing yt on Mac OSX Lion
by Jun-Hwan Choi 21 May '12

21 May '12

Hi yt users, I try to install yt in Mac OS lion and encounter failure. The yt_install.log shows following message at the end of log: ....... running install_egg_info Writing /Users/jhchoi/common/lib/python2.7/lib-dynload/Python-2.7.2-py2.7.egg-info if test -f /Users/jhchoi/common/bin/python -o -h /Users/jhchoi/common/bin/python; \ then rm -f /Users/jhchoi/common/bin/python; \ else true; \ fi (cd /Users/jhchoi/common/bin; ln python2.7 python) rm -f /Users/jhchoi/common/bin/python-config (cd /Users/jhchoi/common/bin; ln -s python2.7-config python-config) test -d /Users/jhchoi/common/lib/pkgconfig || /usr/bin/install -c -d -m 755 /Users/jhchoi/common/lib/pkgconfig rm -f /Users/jhchoi/common/lib/pkgconfig/python.pc (cd /Users/jhchoi/common/lib/pkgconfig; ln -s python-2.7.pc python.pc) /usr/bin/install -c -m 644 ./Misc/python.man \ /Users/jhchoi/common/share/man/man1/python2.7.1 Traceback (most recent call last): File "setup.py", line 418, in <module> version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0].splitlines()[0] IndexError: list index out of range I use the most updated install_script.sh from yt web page. F.Y.I. I install gcc and g++ through Xcode(xcode_432_lion.dmg) w/ command line tools (cltools_lion_latemarch12.dmg). Thanks in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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error while installing yt on Mac OSX Lion
by Jun-Hwan Choi 21 May '12

21 May '12

Hi yt users, I try to install yt in Mac OS lion and encounter failure. The yt_install.log shows following message at the end of log: ....... running install_egg_info Writing /Users/jhchoi/common/lib/python2.7/lib-dynload/Python-2.7.2-py2.7.egg-info if test -f /Users/jhchoi/common/bin/python -o -h /Users/jhchoi/common/bin/python; \ then rm -f /Users/jhchoi/common/bin/python; \ else true; \ fi (cd /Users/jhchoi/common/bin; ln python2.7 python) rm -f /Users/jhchoi/common/bin/python-config (cd /Users/jhchoi/common/bin; ln -s python2.7-config python-config) test -d /Users/jhchoi/common/lib/pkgconfig || /usr/bin/install -c -d -m 755 /Users/jhchoi/common/lib/pkgconfig rm -f /Users/jhchoi/common/lib/pkgconfig/python.pc (cd /Users/jhchoi/common/lib/pkgconfig; ln -s python-2.7.pc python.pc) /usr/bin/install -c -m 644 ./Misc/python.man \ /Users/jhchoi/common/share/man/man1/python2.7.1 Traceback (most recent call last): File "setup.py", line 418, in <module> version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0].splitlines()[0] IndexError: list index out of range I use the most updated install_script.sh from yt web page. F.Y.I. I install gcc and g++ through Xcode(xcode_432_lion.dmg) w/ command line tools (cltools_lion_latemarch12.dmg). Thanks in advance, Junhwan -- -------------------------------------------------------------- Jun-Hwan Choi, Ph.D. Department of Physics and Astronomy, University of Kentucky Tel: (859) 897-6737 Fax: (859) 323-2846 Email: jhchoi(a)pa.uky.edu URL: http://www.pa.uky.edu/~jhchoi --------------------------------------------------------------

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data format supported by yt
by Xiaocheng Zou 20 May '12

20 May '12

Hi, According the online document, yt can support following data format - Enzo Data<http://yt-project.org/docs/2.3/analyzing/loading_data.html#enzo-data> - Orion Data<http://yt-project.org/docs/2.3/analyzing/loading_data.html#orion-data> - FLASH Data<http://yt-project.org/docs/2.3/analyzing/loading_data.html#flash-data> - RAMSES Data<http://yt-project.org/docs/2.3/analyzing/loading_data.html#ramses-data> - ART Data<http://yt-project.org/docs/2.3/analyzing/loading_data.html#art-data> I know enzo data, but how about the other data, what's corresponding simulation produce such data format? Among these simulation, is there any simulation using adaptive mesh refinement method? Last question: i briefly looked at the visualization and data analysis part of yt, it seems that it is out of my expectation. does yt has visualization that will show data evolution when time changes ( i assume data is Adaptive mesh refinement data) ? maybe it is overlap with the simulation? thanks xiaocheng

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Inverted image
by Massimo Gaspari 16 May '12

16 May '12

Hi guys, After a projection and a FixedResolutionBuffer like this: proj = pf.h.proj(axis, "Temperature", None)frb1 = FixedResolutionBuffer(proj, (xmin,xmax,ymin,ymax), res)write_image(na.log10(frb1["Temperature"]), "output.png") I see an inverted image (my computational box is half a cube, z>0 only):http://i.imgur.com/AqWKD.png Is the problem in write_image? Or inside the projection/FRB?How to fix this (without transpose)? Thanks, Max

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curious warning message in parallelHOP
by Geoffrey So 10 May '12

10 May '12

I got this warning message when running paralllel HOP, which I guess was there before but never noticed before because it's close to the top (usually looking at the bottom of the logs). I was wondering if there's anything I need to worry about? -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: lens51 (PID 6818) MPI_COMM_WORLD rank: 323 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- [lens6:19012] 447 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork [lens6:19012] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [lens6:19012] 32 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork [lens6:19012] 32 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork From G.S.

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