Mailman 3 December 2011 - yt-users

Accessing less refined grids
by Elizabeth Tasker 12 Dec '11

12 Dec '11

Hi, Is there an easy way of grabbing the value of the grid above (one less refined) than the current one? e.g. if I had the grid and cell number of a cell, could I deduce the grid and cell number of its parent? I need to look at a smoothed field, which I could calculate, but it would just be equivalent to the less refined level, so I wondered if there was an easier way. Elizabeth

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Strange parallel error
by david collins 07 Dec '11

07 Dec '11

Hi, all-- I'm doing something that I believe to be relatively straight forward, but it's giving me an odd paralllelism error. The initial DomainRightEdge = 0.1 0.1 0.1, changing this to [1,1,1] fixes the problem. I was under the impression that yt was able to do non 0-1 boxes, am I doing something else dumb? Thanks, d. from yt.mods import * pf = load('/scratch/david_c/Paper10/j01_hydro_32/CD0000/cycle0000') pc=PlotCollection(pf,center=[0.5]*3) pc.add_slice('Density',0) Traceback (most recent call last): File "derp.py", line 4, in <module> pc.add_slice('Density',0) File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/visualization/plot_collection.py", line 405, in add_slice center=center, **field_parameters) File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/data_objects/data_containers.py", line 975, in __init__ self._refresh_data() File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/data_objects/data_containers.py", line 293, in _refresh_data self.get_data() File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/data_objects/data_containers.py", line 803, in get_data self._generate_coords() File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/data_objects/data_containers.py", line 1009, in _generate_coords for grid in self._get_grids(): File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 787, in _get_grids return ObjectIterator(self, attr='_grids') File "/usr/projects/magnetic/david_c/local/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 127, in __init__ if hasattr(gs[0], 'proc_num'): IndexError: index out of bounds >>> pdb.pm() > /usr/projects/magnetic/david_c/local/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py(127)__init__() -> if hasattr(gs[0], 'proc_num'): (Pdb) print gs [] ? d. -- Sent from my computer.

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Issues with Enzo 2.0 and YT
by Hadayat Seddiqi 07 Dec '11

07 Dec '11

Hello everyone, I am having issues using simple plot scripts and commands in YT. I would like to know if the YT cookbooks and examples are suitable for use with the newest enzo release. Even the 'yt plot -p {path}' command doesn't give proper plots (it's just a bunch of grid-lines with some bigger squares... nothing like anything I am expecting). If it would help, I can upload a few examples. To be more specific, I've tried this with our own code (GalaxySimulation, though modified) as well as the example problem RotatingCylinder. I would expect that the example problem would run properly without a hitch, but no dice (these are all projections or slices, by the way). I'm wondering if anyone has successfully used YT for these simulations, and if they can provide any useful scripts (or just tell me which of the examples ought to be working). **As a side note, I should mention that when I run YT, I get a bunch of 'divide by zeroes'. I also get a segmentation fault at the very end, but this doesn't seem to affect anything important. In fact, I'm able to run the test data files that come with YT perfectly, even with these 'errors'. For these reasons, I would think that YT isn't the problem.

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yt installation script fails with the message "usr/bin/ld: cannot find -lgcc_s"
by Prasanth 06 Dec '11

06 Dec '11

Hello, I had gfortran already installed, but yt script was using g77. I enabled the line NUMPY_ARGS="--fcompiler=gnu95" in the script, and now it works. [I didn't receive reply to my query in my email account due to list settings. So I am sending a new mail as reply. Sorry about this.] Thanks very much, Prasanth

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yt installation script fails with the message "usr/bin/ld: cannot find -lgcc_s".
by Prasanth 06 Dec '11

06 Dec '11

Hello, The yt installation script fails with the message "usr/bin/ld: cannot find -lgcc_s" . I am running Ubuntu 11.04. The script is the one at http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh, and I ran it a few hours ago. The full yt_install.log is very large and I can't upload it to pastebin.com. Let me know if these is a way of sharing it. I am including a few lines from the beginning and the end of yt_install.log. The first few lines from yt_install.log: df5-1.8.6.tar.gz: OK zlib-1.2.3.tar.bz2: OK bzip2-1.0.5.tar.gz: OK libpng-1.2.43.tar.gz: OK freetype-2.4.4.tar.gz: OK sqlite-autoconf-3070500.tar. gz: OK Python-2.7.1.tgz: OK numpy-1.5.1.tar.gz: OK matplotlib-1.0.0.tar.gz: OK mercurial-1.8.1.tar.gz: OK ipython-0.10.tar.gz: OK h5py-1.3.1.tar.gz: OK Cython-0.14.tar.gz: OK Forthon-0.8.4.tar.gz: OK ext-3.3.2.zip: OK ext-slate-110328.zip: OK PhiloGL-1.1.0.zip: OK If compilation produces errors, or a large number of warnings, please read README.COMPILATION.PROBLEMS -- you might be able to adjust the flags in this Makefile to improve matters. Also in README.COMPILATION.PROBLEMS are some hints that may help if your build produces an executable which is unable to correctly handle so-called 'large files' -- files of size 2GB or more. Last few lines from yt_install.log: creating build/temp.linux-i686-2.7/numpy/linalg compile options: '-DATLAS_INFO="\"3.8.3\"" -I/usr/include/atlas -Inumpy/core/include -Ibuild/src.linux-i686-2.7/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/home/phn/Downloads/yt-i686/include/python2.7 -Ibuild/src.linux-i686-2.7/numpy/core/src/multiarray -Ibuild/src.linux-i686-2.7/numpy/core/src/umath -c' gcc: numpy/linalg/python_xerbla.c as: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so) gcc: numpy/linalg/lapack_litemodule.c as: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so) /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-i686-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-i686-2.7/numpy/linalg/python_xerbla.o -L/usr/lib/atlas-base/atlas -L/usr/lib/atlas-base -Lbuild/temp.linux-i686-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-i686-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so ) /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status /usr/bin/ld: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so ) /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-i686-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-i686-2.7/numpy/linalg/python_xerbla.o -L/usr/lib/atlas-base/atlas -L/usr/lib/atlas-base -Lbuild/temp.linux-i686-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-i686-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 Thanks, Prasanth

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Yt installation fails with the message "usr/bin/ld: cannot find -lgcc_s".
by Prasanth 05 Dec '11

05 Dec '11

Hello, The yt installation script fails with the message "usr/bin/ld: cannot find -lgcc_s" . I am running Ubuntu 11.04. The script is the one at http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh, and I ran it a few minutes ago. The full yt_install.log is very large and I can't upload it to pastebin.com. Let me know if these is a way of sharing it. I am including a few lines from the beginning and the end of yt_install.log. The first few lines from yt_install.log: df5-1.8.6.tar.gz: OK zlib-1.2.3.tar.bz2: OK bzip2-1.0.5.tar.gz: OK libpng-1.2.43.tar.gz: OK freetype-2.4.4.tar.gz: OK sqlite-autoconf-3070500.tar.gz: OK Python-2.7.1.tgz: OK numpy-1.5.1.tar.gz: OK matplotlib-1.0.0.tar.gz: OK mercurial-1.8.1.tar.gz: OK ipython-0.10.tar.gz: OK h5py-1.3.1.tar.gz: OK Cython-0.14.tar.gz: OK Forthon-0.8.4.tar.gz: OK ext-3.3.2.zip: OK ext-slate-110328.zip: OK PhiloGL-1.1.0.zip: OK If compilation produces errors, or a large number of warnings, please read README.COMPILATION.PROBLEMS -- you might be able to adjust the flags in this Makefile to improve matters. Also in README.COMPILATION.PROBLEMS are some hints that may help if your build produces an executable which is unable to correctly handle so-called 'large files' -- files of size 2GB or more. Last few lines from yt_install.log: creating build/temp.linux-i686-2.7/numpy/linalg compile options: '-DATLAS_INFO="\"3.8.3\"" -I/usr/include/atlas -Inumpy/core/include -Ibuild/src.linux-i686-2.7/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/home/phn/Downloads/yt-i686/include/python2.7 -Ibuild/src.linux-i686-2.7/numpy/core/src/multiarray -Ibuild/src.linux-i686-2.7/numpy/core/src/umath -c' gcc: numpy/linalg/python_xerbla.c as: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so) gcc: numpy/linalg/lapack_litemodule.c as: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so) /usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-i686-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-i686-2.7/numpy/linalg/python_xerbla.o -L/usr/lib/atlas-base/atlas -L/usr/lib/atlas-base -Lbuild/temp.linux-i686-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-i686-2.7/numpy/linalg/lapack_lite.so /usr/bin/ld: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so ) /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status /usr/bin/ld: /home/phn/Downloads/yt-i686/lib/libz.so.1: no version information available (required by /usr/lib/libbfd-2.21.0-system.20110327.so ) /usr/bin/ld: cannot find -lgcc_s collect2: ld returned 1 exit status error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-i686-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-i686-2.7/numpy/linalg/python_xerbla.o -L/usr/lib/atlas-base/atlas -L/usr/lib/atlas-base -Lbuild/temp.linux-i686-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-i686-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 Thanks, Prasanth

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Streamlines and arc length
by John ZuHone 03 Dec '11

03 Dec '11

Hi all, Does anyone know how to get an arc length out of the streamlines? t is dimensionless but must be related to it somehow. Best, John

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yt bootstrap
by Elizabeth Tasker 02 Dec '11

02 Dec '11

Hi, I tried to start the yt development bootstrap tool on my mac, but get the following error: *** The yt-supplemental repository is not checked *** *** out. I can do this for you, but because this *** *** is a delicate act, I require you to respond *** *** to the prompt with the word 'yes'. *** Do you want me to try to check it out? yes Traceback (most recent call last): File "./yt", line 9, in <module> load_entry_point('yt==2.3dev', 'console_scripts', 'yt')() File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/command_line.py", line 1609, in run_main sys.exit(YT.main()) File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/cmdln.py", line 257, in main return self.cmd(args) File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd retval = self.onecmd(argv) File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd return self._dispatch_cmd(handler, argv) File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd return handler(argv[0], opts, *args) File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/command_line.py", line 907, in do_bootstrap_dev supp_path = _get_yt_supp() File "/Users/pergamond/yt/yt/src/yt-hg/yt/utilities/command_line.py", line 349, in _get_yt_supp rv = commands.clone(uu, NameError: global name 'commands' is not defined Any ideas? Elizabeth

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pickle
by Elizabeth Tasker 02 Dec '11

02 Dec '11

Hi, A bigger problem.... The lastest version of yt The current version of the code is: --- a519b8754ba8 (yt) tip --- has problems with pickle. If I pickle a data set and then try and unpickle it, I see: unpickle core data --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/tasker/yt/src/yt-hg/scripts/iyt in <module>() 338 339 #file = open('cores.pickle','rb') --> 340 allcloudcores = cPickle.load(file('cores.pickle', 'rb')) 341 file.close() 342 /home/tasker/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs) 3676 else: new_args.append(arg) 3677 pfs = ParameterFileStore() -> 3678 pf = pfs.get_pf_hash(pfid) 3679 cls = getattr(pf.h, dtype) 3680 obj = cls(*new_args) /home/tasker/yt/src/yt-hg/yt/utilities/parameter_file_storage.pyc in get_pf_hash(self, hash) 106 def get_pf_hash(self, hash): 107 """ This returns a parameter file based on a hash. """ --> 108 return self._convert_pf(self._records[hash]) 109 110 def get_pf_ctid(self, ctid): KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function _reconstruct_object at 0x272c938>, ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16., 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]), {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16., 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector': array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1358, 0.1716, 0.2074, 0.2432, 0.279 , The fact it mentions the field parameters in the last line, might mean it's an error introduced because of the corrections to them (that I have been demanding!)? The script I have works fine (pickles and all) on yt version: --- 16e8d749a806 (yt) tip --- Elizabeth

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field parameters (you know I want to use them everywhere...)
by Elizabeth Tasker 01 Dec '11

01 Dec '11

Hi, Two small problems: 1. Another issue with field parameters. I can't pass them to a slice if the derived field also needs ValidateSpatial. i.e. def _EffectivePotential(field, data): center = na.array(data.get_field_parameter("disk_center")) h_vec = na.array(data.get_field_parameter("disk_vector")) omega = na.array(data.get_field_parameter("thiscore_omega")) . . blah . . add_field("EffectivePotential", function=_EffectivePotential, validators=[ValidateSpatial(1, ["x-velocity", "y-velocity", "z-velocity", "x", "y", "z"])]) p = pc.add_slice("EffectivePotential", 2, field_parameters={"disk_vector":disk_vector, "disk_center":disk_center, "thiscore_omega":core_omega[c]}) can't find its field parameters but if I change the end line of the function to: add_field("EffectivePotential", function=_EffectivePotential) everything is fine. It actually seems to work OK even without the ValidateSpatial (I have cross products in the function so pain has the potential to happen without the full data) so perhaps this isn't a problem, but I think it is a small bug? 2. For some reason, yt has decided to save all my image files in: /home/tasker/.yt/my_plugins.py_Slice_z_EffectivePotential.png This is less than intuitive. Does anyone know why and how I can stop it? Thanks! Elizabeth

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