Mailman 3 March 2013 - yt-dev

Units
by Matthew Turk 07 Mar '13

07 Mar '13

Hi all, Casey, Anna, Nathan, Britton and I have been working on units in 3.0, based on the stuff Casey's worked on before. Anna submitted a YTEP here: https://bitbucket.org/yt_analysis/ytep/pull-request/13/created-new-ytep-for… Comments on this would help shape the direction. We're currently knee-deep in the implementation details, but hopefully this will be in a workable state by the end of the workshop. -Matt

1 0

[yt_analysis/yt] installation problem: unrecognized command line option ‘-faltivec’ (issue #518)
by jcpassy 07 Mar '13

07 Mar '13

--- you can reply above this line --- New issue 518: installation problem: unrecognized command line option ‘-faltivec’ https://bitbucket.org/yt_analysis/yt/issue/518/installation-problem-unrecog… jcpassy: Hi all, running the current development install script on OSX 10.8.2 fails when installing numpy: ------------------------------------------------------------------------------------------------------------ Installing numpy-1.6.1 (arguments: 'numpy-1.6.1 --fcompiler=gnu95') ******************************************** FAILURE REPORT: ******************************************** compiling C sources C compiler: gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes creating build/temp.macosx-10.4-x86_64-2.7/numpy/core/blasdot compile options: '-DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Users/jcpassy/Work/yt-x86_64/include/python2.7 -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/umath -c' extra options: '-faltivec -I/System/Library/Frameworks/vecLib.framework/Headers' gcc: numpy/core/blasdot/_dotblas.c gcc.exec: error: unrecognized command line option ‘-faltivec’ gcc.exec: error: unrecognized command line option ‘-faltivec’ error: Command "gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DNO_ATLAS_INFO=3 -Inumpy/core/blasdot -Inumpy/core/include -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Users/jcpassy/Work/yt-x86_64/include/python2.7 -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.macosx-10.4-x86_64-2.7/numpy/core/src/umath -c numpy/core/blasdot/_dotblas.c -o build/temp.macosx-10.4-x86_64-2.7/numpy/core/blasdot/_dotblas.o -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1 ------------------------------------------------------------------------------------------------------------ I am using gcc 4.7.2 which I got from http://www.astro.wisc.edu/~townsend/static.php?ref=mesasdk#Mac_OS_X Thanks a lot, JC -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

1 0

summing over phase plot and total quantity discrepancies
by Geoffrey So 06 Mar '13

06 Mar '13

I'm trying to use add_phase_object to get a 2D distribution and summing over the y axis to see the total quantity in each x bins. I am using the old plot collection to do the phase distribution because it is parallelized, the binned2D is serial I believe. I'm checking the numbers by using TotalQuantity which sums all the cells in the simulation, and I should get the same number when I sum over the color axis of the phase plot (I'm assuming this is true, can someone also verify the logic?), but I am getting slightly different number. More curious, is when the y axis is the same as the color axis, I get different numbers as when the axis names are different. I first saw the discrepancy using other fields, but in this script I am demonstrating with fields that everyone should have access to in an Enzo simulation. http://paste.yt-project.org/show/3222/ Can someone run the script very quick and verify that they get different numbers printed on screen? Is there an easier way to do what I'm trying to do in parallel? From G.S. PS: This issue is in both dev-yt I have on my laptop and on Gordon my laptop uses: changeset: 6566:6794b2798b5a branch: yt tag: tip user: Matthew Turk <matthewturk(a)gmail.com> date: Wed Oct 24 15:58:34 2012 -0400 summary: Swap out get_smallest_dx for 8192. Should fix the buildbot. Gordon I have: changeset: 7124:4151cc9ff9b2 branch: yt tag: tip user: Kacper Kowalik <xarthisius.kk(a)gmail.com> date: Sat Feb 02 11:03:07 2013 +0100 files: yt/utilities/logger.py description: Add `NullHandler` to `ytLogger` when stream logging is suppresed. Fixes #492

2 2

Please don't delete your repositories
by Matthew Turk 06 Mar '13

06 Mar '13

Hi everyone, This is an empassioned plea not to delete your repositories, especially if they have been the subject of pull requests -- successful or not. Once a repository has been deleted, all comments and code review are now gone. They can be reconstructed from email, but are otherwise lost. I've talked to BB support, and they suggested we open a feature request, but right now this is how things are. So please, once you have created a repo that forms the basis of one or more pull requests, please don't delete it. -Matt

3 3

[yt_analysis/yt] Boolean objects can't be pickled (issue #517)
by Matthew Turk 05 Mar '13

05 Mar '13

--- you can reply above this line --- New issue 517: Boolean objects can't be pickled https://bitbucket.org/yt_analysis/yt/issue/517/boolean-objects-cant-be-pick… Matthew Turk: A typo in `_con_args` prevents boolean objects from being pickled. -- This is an issue notification from bitbucket.org. You are receiving this either because you are the owner of the issue, or you are following the issue.

1 0

Good benchmark?
by Matthew Turk 04 Mar '13

04 Mar '13

Hi all, I got an email asking for a benchmark of yt. I think this is very, very valuable to have going forward. I was wondering if anyone had any suggestions? I'm thinking that we probably want to test things like the halo finder, projections, and phase plots. Would a medium (1536^3) halo profiling run do that? Do we want to add on some global projections and phase plots as well? -Matt

7 12

Announcing the release of yt 2.5!
by John ZuHone 01 Mar '13

01 Mar '13

Dear Colleagues, We’re proud to announce the release of version 2.5 of the yt Project, http://yt-project.org/. The new version includes many new features, refinements of existing features and numerous bugfixes. We encourage all users to upgrade to take advantage of the changes. yt is a community-developed analysis and visualization toolkit, primarily directed at astrophysical hydrodynamics simulations. It provides full support for output from the Enzo, FLASH, Orion, and Nyx codes, with preliminary support for several others. It provides access to simulation data using an intuitive python interface, can perform many common visualization tasks, and offers a framework for conducting data reductions and analysis of simulation data. The most visible changes with the 2.5 release include: * Testing has been greatly expanded, including unit tests and answer testing. * The capabilities of the “Stream” frontend have been expanded. Uniform grid and AMR-based data can be read into memory, and particle fields can be initialized. * The install script now provides for the optional installation of SciPy and the Rockstar halo finder. * Surfaces can now be extracted and examined, as well as uploaded to Sketchfab.com for interactive visualization in a web browser. * Support for the Athena code has been added. * Many, many improvements to PlotWindow. * Coordinate transformations have been sped up and streamlined, as well as cylindrical and spherical fields. * Increased support for the IPython notebook. * Improved support for FLASH particle fields. * The volume rendering backend has been updated to use an alpha channel, fixing parallel opaque volume renderings. * The AMRKDTree has been rewritten, allowing parallelism with other than power-of-2 MPI processes, arbitrary sets of grids, and splitting of unigrids. For a complete list of changes in this release, please visit the Changelog (http://yt-project.org/docs/2.5/changelog.html). Information about the yt project, including installation instructions, can be found on the homepage: http://yt-project.org/ Development of yt has been sponsored by the NSF, the DOE, and various universities. We develop yt in the open and encourage contributions from users who extend and improve the code. We invite you to get involved with developing and using yt! Please forward this announcement to other interested parties. Sincerely, The yt development team

1 0