Mailman 3 March 2013 - yt-users

installation problem: unrecognized command line option ‘-faltivec’
by Jean-Claude Passy March 7, 2013

March 7, 2013

Hi all, I am having trouble installing the current dev version. I get the following error: * ----------------------------------------------------------------------------------------------------------------------------------- * *Building LAPACK* *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 on OSX 10.8.2, with gcc 4.7.2 (but I have also tried the build-in version 4.2.1). I have tried turning on the different NUMPY_ARGS, but it did not help. Does anybody have an idea how to fix this? Thanks a lot guys, JC

2 2

Trouble with SFR plots of enzo data
by Munier Azzam Salem March 5, 2013

March 5, 2013

Hey Guys, I've been using yt's star analysis module to produce plots of SFR vs. time to compare the star formation histories across multiple runs. It works well except when it doesn't. I've been working with enzo and for late time files (I believe produced after a run was restarted) the star formation history cuts off and drops to 0 for the earlier times. Weirder still, when I open earlier data files and plot them atop, the earlier results disagree! I attached a plot of this below. Does anyone know what's happening here? Is there a better way to do this? best, Munier The Code: *import matplotlib as mpl* *mpl.use('agg')* *import matplotlib.pyplot as plt* *from yt.mods import ** *from yt.analysis_modules.star_analysis.api import ** * * *def SFR(fName,stroke):* * * * # open file* * try:* * pf=load(fName)* * except YTOutputNotIdentified:* * return False* * * * # calculate SFR* * dd = pf.h.all_data()* * sfr = StarFormationRate(pf,data_source=dd)* * * * plt.plot(sfr.time,sfr.Msol_yr,stroke,linewidth=1)* * return ( sfr.time.min() , sfr.time.max() )* * * *MaxVals = []* *SFR("../FIDUCIAL/DD0005/test_sim_0005","k-")* *SFR("../FIDUCIAL/DD0010/test_sim_0010","k-")* *SFR("../FIDUCIAL/DD0017/test_sim_0017","k-")* * * *plt.xlim((1.27E10,1.30E10))* *plt.savefig("SFR")* -- Munier A. Salem // 845.489.6450

7 18

Problems with pickle
by Elizabeth Tasker March 5, 2013

March 5, 2013

Hi, I'm getting a problem with pickle that I've not seen before. I have an extracted_region that I'm trying to pickle via: file = open(('cloud%d_pyfindclouds2.pickle' % p), 'wb') cPickle.dump(cloud, file, protocol=-1) file.close() but I'm getting: In [16]: cPickle.dump(cloud, file, protocol=-1) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) /Users/Elizabeth/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 cPickle.dump(cloud, file, protocol=-1) /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in __reduce__(self) 403 def __reduce__(self): 404 args = tuple([self.pf._hash(), self._type_name] + --> 405 [getattr(self, n) for n in self._con_args] + 406 [self.field_parameters]) 407 return (_reconstruct_object, args) AttributeError: 'AMRBooleanRegion' object has no attribute 'r' Does anyone know what might be causing this? Elizabeth

3 5

Announcing the release of yt 2.5!
by John ZuHone March 1, 2013

March 1, 2013

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

2 1

Test for field
by Elizabeth Tasker March 1, 2013

March 1, 2013

Hi, I want to test if a data set at particles. I thought: pf.has_key("particle_type") would work, but oddly it doesn't since: In [17]: pf.has_key("particle_type") Out[17]: False yet: In [4]: dd = pf.h.all_data() In [5]: dd["particle_type"] yt : [INFO ] 2013-02-23 17:00:43,826 Getting particle_type using ParticleIO Out[5]: array([11, 11, 11, ..., 11, 11, 11]) Shouldn't pf.has_key("particle_type") be true in this case? Elizabeth

3 3