Mailman 3 February 2013 - yt-users

Please help
by Reju Sam John Feb. 20, 2013

Feb. 20, 2013

In the following code (c attachment also) import pylab as P from yt.mods import * pf = load("RD0002/RedshiftOutput0002") c = pf.h.find_max('Density')[1] proj = pf.h.proj(1, 'Density') width = 96/pf['mpc'] # we want a 1.5 mpc view res = [1000, 1000] # create an image with 1000x1000 pixels frb = proj.to_frb(width, res, center=[0.5,0.5,0.5]) P.imshow(frb['Density']) P.xlabel(r'$x\ \mathrm{kpc}$') P.ylabel(r'$x\ \mathrm{furlongs}$') P.savefig('Density_y.png') My problem is to develop a new code which automatically take `n' input files (RD0001/RedshiftOutput0001, RD0002/RedshiftOutput0002, RD0003 /RedshiftOutput0003, ....) and want to save each output files in a folder. Please help me..... -- Reju Sam John

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Visualising spectral cube data in yt
by Francisco Ocaña González Feb. 20, 2013

Feb. 20, 2013

Dear Eli, I found a post about 3D data in YT , http://astrobiased.com/3d-data-vis-in-yt.html , very interesting. I am working with spectral cubes from PMAS Spectrograph (at 3.5m CAHA telescope). Thus, I tried to use it. I am newbie with python, but I was able to install everything :-) However I get an error message when loading the data into yt's data structure (script http://paste.yt-project.org/show/3182/ ): ERROR: ValueError: total size of new array must be unchanged [yt.frontends.stream.data_structures] astropy: [ERROR ] 2013-02-20 10:46:53,395 ValueError: total size of new array must be unchanged Traceback (most recent call last): File "3d_viewer.py", line 9, in <module> pf = load_uniform_grid(data, cube.shape, 9e16) File "/home/fog/YT/yt-x86_64/src/yt-hg/yt/frontends/stream/data_structures.py", line 490, in load_uniform_grid grid_dimensions = domain_dimensions.reshape(nprocs,3).astype("int32") ValueError: total size of new array must be unchanged I have uploaded the cube to: http://bolidox.fis.ucm.es/~alex/YT_cube/ . FITS seems to be quite ok according to the FITS validator. And the 'cube' object is well loaded, I guess. Have you had this problem? Cheers, Paco Ocaña

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ART time
by Pedro Colin Feb. 20, 2013

Feb. 20, 2013

Hi, I have downloaded several ART files and parameters like current redshift or omega lambda are okay but the current time = 4.38272802952e+17 looks very suspicious. This may be the reason why I got an error when I try to print_stats raise KeyError(key) KeyError: 'Time' I also think this error is the reason why I got wrong units. By the way, I know ART time code unit is negative and reached zero at the present time. Any help? Pedro Colin

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yt/ART/two questions
by Pedro Colin Feb. 15, 2013

Feb. 15, 2013

Hi, yt has been installed and I have already done some tests. I can load data from ART but I have run into some problems. At this moment, I have a couple of questions. One of the things that yt can do is to find the maximum of the density field and give you the coordenates of it. The web page says that coordinates are in code units which I guess are yt units, [0,1] in any direction. If this is so, the maximum found by yt does not agree with the one I found with ifrit. A second point is that when I try to compute the "AngularMomentumVector" inside a sphere it gives me an error (with Enzo test data I don't have this problem): my_sphere.quantities["AngularMomentumVector"]() File "/fs/nova/other0/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/field_info_container.py", line 316, in __call__ dd = self._function(self, data) TypeError: _x_velocity() takes exactly 1 argument (2 given) Regards, Pedro

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SciPy 2013 Announcement -- June 24 - 29, 2013, Austin, TX!
by Anthony Scopatz Feb. 15, 2013

Feb. 15, 2013

Hello All, As this years conference communications co-chair, it is my extreme pleasure to announce the *SciPy 2013 conference from June 24th - 29th in sunny Austin, Texas, USA.* Please see our website<http://conference.scipy.org/scipy2013/about.php>(or below) for more details. A call for presentations, tutorials, and papers will be coming out very soon. Please make sure to sign up on our mailing list<http://eepurl.com/dyoeL>, follow us on twitter <https://twitter.com/SciPy2013>, or Google Plus<https://plus.google.com/u/0/100948873231627513165/posts> so that you don't miss out on any important updates. I sincerely hope that you can attend this year and make 2013 the best year for SciPy yet! Happy Hacking! Anthony Scopatz SciPy 2013 Conference Announcement ---------------------------------- SciPy 2013, the twelfth annual Scientific Computing with Python conference, will be held this June 24th-29th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The conference consists of two days of tutorials by followed by two days of presentations, and concludes with two days of developer sprints on projects of interest to the attendees. Specialized Tracks ------------------ This year we are happy to announce two specialized tracks run in parallel to the general conference: *Machine Learning* In recent years, Python's machine learning libraries rapidly matured with a flurry of new libraries and cutting-edge algorithm implement and development occurring within Python. As Python makes these algorithms more accessible, machine learning algorithm application has spread across disciplines. Showcase your favorite machine learning library or how it has been used as an effective tool in your work! *Reproducible Science* Over recent years, the Open Science movement has stoked a renewed acknowledgement of the importance of reproducible research. The goals of this movement include improving the dissemination of progress, prevent fraud through transparency, and enable deeper/wider development and collaboration. This track is to discuss the tools and methods used to achieve reproducible scientific computing. Domain-specific Mini-symposia ----------------------------- Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: - Meteorology, climatology, and atmospheric and oceanic science - Astronomy and astrophysics - Medical imaging - Bio-informatics Tutorials --------- Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, targeting specifically programmers with no prior knowledge of scientific python. Developer Sprints ----------------- A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and recieve tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. Birds-of-a-Feather (BOF) Sessions --------------------------------- Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. Important Dates --------------- - March 18th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. - April 15th: Speakers selected - April 22nd: Sponsorship acceptance deadline - May 1st: Speaker schedule announced - May 5th: Paper submission deadline - May 6th: Early-bird registration ends - June 24th-29th: 2 days of tutorials, 2 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all at the conference. The SciPy2013 organization team: * Andy Terrel, Co-chair * Jonathan Rocher, Co-chair * Katy Huff, Program Committee co-chair * Matt McCormick, Program Committee co-chair * Dharhas Pothina, Tutorial co-chair * Francesc Alted, Tutorial co-chair * Corran Webster, Sprint co-chair * Peter Wang, Sprint co-chair * Matthew Turk, BoF co-chair * Jarrod Millman, Proceeding co-chair * Stéfan van der Walt, Proceeding co-chair * Anthony Scopatz, Communications co-chair * Majken Tranby, Communications co-chair * Jeff Daily, Financial Aid co-chair * John Wiggins, Financial Aid co-chair * Leah Jones, Operations chair * Brett Murphy, Sponsor chair * Bill Cowan, Financial chair

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Install script failure under OpenSuSE 12.2
by Erik Rosolowsky Feb. 14, 2013

Feb. 14, 2013

Dear List -- I had some build issues with yt on OpenSuSE 12.2 which likely affect users of >12.1 Python apparently builds critical components into $YT_DEST/lib64/python2.7/config/ $YT_DEST/lib64/python2.7/lib-dynload/ and then looks for them in: $YT_DEST/lib/python2.7/config/ $YT_DEST/lib/python2.7/lib-dynload/ resulting in this failure when the script tried to build distribute. Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 563, in <module> main() File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 545, in main known_paths = addusersitepackages(known_paths) File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 278, in addusersitepackages user_site = getusersitepackages() File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 253, in getusersitepackages user_base = getuserbase() # this will also set USER_BASE File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/site.py", line 243, in getuserbase USER_BASE = get_config_var('userbase') File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 521, in get_config_var return get_config_vars().get(name) File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 420, in get_config_vars _init_posix(_CONFIG_VARS) File "/UBC-O/erosolo/yt-x86_64/lib/python2.7/sysconfig.py", line 288, in _init_posix raise IOError(msg) IOError: invalid Python installation: unable to open /UBC-O/erosolo/yt-x86_64/lib/python2.7/config/Makefile (No such file or directory) I patched the problem by symbolically linking the lib64/python2.7 files into the lib/python2.7 directories and re-executing the script. Is there a better approach to this fail? thank you, e. -- Erik Rosolowsky Asst. Prof. of Physics and Astronomy University of British Columbia Okanagan 3333 University Way, Kelowna BC V1V 1V7 Canada (250) 807-9623 - erik.rosolowsky(a)ubc.ca

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using Intel compilers
by Mark Kremenetsky Feb. 9, 2013

Feb. 9, 2013

Folks, i am trying to set up ENZO environment using Intel compilers and not default gcc, gfort, etc I am using install_script.sh script. Does somebody know how to change the choice of a compiler that will be used in order to build HDF5, Python, etc needed for ENZO compilation. Thanks in advance, Mark

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eps_writer question
by Jun-Hwan Choi Feb. 8, 2013

Feb. 8, 2013

Hi yt user, This question mostly goes to John Wise (maybe not). I try to use eps_writer module in the yt to generate a high-quality .eps figure. I attempt to make four phase plot (rho-T) from four different times (i.e. four different data output) But, I got the following error message: File "Phase_eps.py", line 39, in <module> ep = eps.multiplot_yt(2,2,pc) File "/home/jhchoi/common/lib/python2.7/site-packages/yt-2.4-py2.7-linux-x86_64.egg/yt/visualization/eps_writer.py", line 1010, in multiplot_yt "x ncol(%d)." % (len(plot_col.plots), nrow, ncol) TypeError: not all arguments converted during string formatting It look that there is a problem when I over write PlotCollection object for four different data output (or maybe not). How can I solve the issue? I paste my script at http://paste.yt-project.org/show/3112/ . In addition, I would like to get more information/document about eps_writer. For example, I would like to write the time of four phase respectively. Where can I get the information about it? Thank you 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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install script fails!
by Suresh Shelvapille Feb. 7, 2013

Feb. 7, 2013

Dear Folks: I am new to YT and I was trying to install YT using the install script. And it fails with the following error: I have cut and pasted lines of the log: ----------------------------------------------------------- Installing BZLIB Installing ZLIB Installing PNG Installing FreeType2 Installing HDF5 Installing SQLite3 Installing Python. This may take a while, but don't worry. YT loves you. Installing Mercurial. Installing mercurial-2.2.2 (arguments: 'mercurial-2.2.2') Setting YT_DIR=/home/labuser/exp_ib_tests/yt-x86_64/src/yt-hg/ Installing distribute ******************************************** FAILURE REPORT: ******************************************** return self.readnormal(size) File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/tarfile.py", line 744, in readnormal return self.fileobj.read(size) File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 252, in read self._read(readsize) File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 299, in _read self._read_eof() File "/home/labuser/exp_ib_tests/yt-x86_64/lib/python2.7/gzip.py", line 338, in _read_eof hex(self.crc))) IOError: CRC check failed 0x900b50a1 != 0x35489988L ******************************************** ******************************************** Failure. Check /home/labuser/exp_ib_tests/yt-x86_64/yt_install.log. The last 10 lines are above. Any help would be great! Many thanks, Suri

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Fwd: [Yt-dev] saving derived fields
by Andrew Myers Feb. 7, 2013

Feb. 7, 2013

Hello YT users, A couple of years ago, Sam Skillman (email chain attached) asked about support for saving derived fields to the disk, so we don't have to re-compute expensive fields over and over again. Did this functionality ever make it into yt? I'm working on something where this would be very useful, so if not I might have a go at implementing myself. Thanks, Andrew Myers ---------- Forwarded message ---------- From: Sam Skillman <samskillman(a)gmail.com> Date: Tue, Jan 11, 2011 at 9:40 AM Subject: [Yt-dev] saving derived fields To: yt-dev(a)lists.spacepope.org Hi all, I've started dealing with a lot of time-consuming derived fields and am wondering if there is already support for writing derived fields back to the raw data files (e.g. .cpu files). If not, any thoughts on doing so? Sam _______________________________________________ Yt-dev mailing list Yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

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