Mailman 3 April 2013 - yt-dev

[yt_analysis/yt] Projections should switch off parallel reduction method (issue #549)
by Matthew Turk 15 Apr '13

15 Apr '13

New issue 549: Projections should switch off parallel reduction method https://bitbucket.org/yt_analysis/yt/issue/549/projections-should-switch-of… Matthew Turk: For those simulation types where the global mesh is known, we should use the (slightly more scalable) global mesh information to pre-construct the quadtree which is then reduced as an array across all processors. For those simulation types where we do not know the global mesh information, we should fall back on the quadtree reduction method we used before, which is in the routine `merge_quadtree_buffers` in `parallel_analysis_interface`. This will require a flag or some type of discriminator between global/local mesh simulations. Responsible: MatthewTurk

1 0

[yt_analysis/yt] Fisheye camera does not work (issue #548)
by Matthew Turk 15 Apr '13

15 Apr '13

New issue 548: Fisheye camera does not work https://bitbucket.org/yt_analysis/yt/issue/548/fisheye-camera-does-not-work Matthew Turk: The changes to get opacity working were not propagated to the fisheye camera. Responsible: MatthewTurk

1 0

[yt_analysis/yt] Standardize arguments to plot annotations (issue #547)
by Matthew Turk 15 Apr '13

15 Apr '13

New issue 547: Standardize arguments to plot annotations https://bitbucket.org/yt_analysis/yt/issue/547/standardize-arguments-to-plo… Matthew Turk: `plot_args` and `text_args` should only be one or the other. Having multiple argument names is confusing. Responsible: MatthewTurk

1 0

push_with_ids
by Matthew Turk 13 Apr '13

13 Apr '13

Hi all (especially Sam and Stephen, who have done a lot of this type of debugging), Christine and I sat down in person, and set up some tracers throughout the code to see where her inline with yt was dying. It looks like it's in this call: communication_system.push_with_ids(ranks) Can either of you think why this might be a problem? I thought MVAPICH supported everything we use, but if this is dying, that could be an issue. Sam, if she's using the Enzo with the refactored communicator, could that be an issue here? Any ideas? ...all the more reason for an isolated, over-the-wire interface library... -Matt

3 3

[yt_analysis/yt] Clump finding doesn't use chunks (issue #546)
by Christopher Moody 09 Apr '13

09 Apr '13

New issue 546: Clump finding doesn't use chunks https://bitbucket.org/yt_analysis/yt/issue/546/clump-finding-doesnt-use-chu… Christopher Moody: Clump-finding is broken for the chunk system; currently IsBound returns pot/kin for every chunk. This fails spectacularly when the chunking goes level-by-level, where we only include cells at the same levels in the potential calculation. Instead, it should add every chunk to a persistent octree, and in the combine step it should calculate the binding energy. Responsible: juxtaposicion -- 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.

2 1

[yt_analysis/yt] yt clobbers nose's command line help (issue #545)
by Nathan Goldbaum 08 Apr '13

08 Apr '13

New issue 545: yt clobbers nose's command line help https://bitbucket.org/yt_analysis/yt/issue/545/yt-clobbers-noses-command-li… Nathan Goldbaum: ``` #!bash $ nosetests --help usage: nosetests [-h] [--config CONFIG] [--paste] [--paste-detailed] [--detailed] [--rpdb] [--parallel] yt command line arguments optional arguments: -h, --help show this help message and exit --config CONFIG Set configuration option, in the form param=value --paste Paste traceback to paste.yt-project.org --paste-detailed Paste a detailed traceback with local variables to paste .yt-project.org --detailed Display detailed traceback. --rpdb Enable remote pdb interaction (for parallel debugging). --parallel Run in MPI-parallel mode (must be launched as an MPI task) ``` Responsible: ngoldbaum -- 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

[yt_analysis/yt] Chombo answer test results are too big (issue #544)
by Nathan Goldbaum 07 Apr '13

07 Apr '13

New issue 544: Chombo answer test results are too big https://bitbucket.org/yt_analysis/yt/issue/544/chombo-answer-test-results-a… Nathan Goldbaum: Right now the chombo answer test results are way too big: ``` #!bash $ ls -lh gold007_data* -rw-r--r-- 1 goldbaum staff 104M Mar 30 05:58 gold007_data.0005.3d.hdf5 -rw-r--r-- 1 goldbaum staff 259M Mar 30 05:41 gold007_data.0077.3d.hdf5 ``` For comparison: ``` #!bash $ ls -lh gold007_moving_0010 gold007_galaxy0030 -rw-r--r-- 1 goldbaum staff 23M Mar 30 05:39 gold007_moving7_0010 -rw-r--r-- 1 goldbaum staff 43M Mar 30 05:37 gold007_galaxy0030 ``` -- 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

[yt_analysis/yt] annotate_particles doesn't respect periodicity (issue #543)
by Sam Skillman 05 Apr '13

05 Apr '13

New issue 543: annotate_particles doesn't respect periodicity https://bitbucket.org/yt_analysis/yt/issue/543/annotate_particles-doesnt-re… Sam Skillman: Annotating particles should use periodic calculations. This can be seen by setting the center of the plot to something other than the domain: ``` #!python from yt.mods import * pf = load('Enzo_64/DD0043/data0043') p = ProjectionPlot(pf, 0, 'Ones', center=[0.75]*3) p.annotate_particles(0.1) p.save() ``` -- 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

[yt_analysis/yt] Standard deviation fields for profiles are undocumented (issue #542)
by Nathan Goldbaum 04 Apr '13

04 Apr '13

New issue 542: Standard deviation fields for profiles are undocumented https://bitbucket.org/yt_analysis/yt/issue/542/standard-deviation-fields-fo… Nathan Goldbaum: We should add docs and cookbook recipes on generating profiles of fields that are the standard deviation of an on-disk or derived fields. For me, this is most interesting for calculating velocity dispersion profiles. This functionality was originally added in PR 114, but unfortunately bitbucket won't render any accompanying information that came with the PR. I've provisionally assigned this to Britton. Britton, please let me know if you're too busy and I'll try to figure it out. Responsible: brittonsmith -- 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.

2 1

[yt_analysis/yt] Docs for Ghost Zone Requiring Covering Grids (issue #541)
by Sam Skillman 04 Apr '13

04 Apr '13

New issue 541: Docs for Ghost Zone Requiring Covering Grids https://bitbucket.org/yt_analysis/yt/issue/541/docs-for-ghost-zone-requirin… Sam Skillman: We should make it clear how to get a covering grid for fields that require ghost zones. This is primarily a docs issue, but the By running the cookbook ``extract_fixed_resolution_data.py`` with DivV instead leads to this error: ``` #!python skillman/test_data:python extract_fixed_resolution_data.py Traceback (most recent call last): File "extract_fixed_resolution_data.py", line 19, in <module> num_ghost_zones=0) File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3735, in __init__ self._refresh_data() File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3752, in _refresh_data AMR3DData._refresh_data(self) File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 320, in _refresh_data self.get_data() File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3770, in get_data self._generate_field(field) File "/home/skillman/local/src/yt-hg/yt/data_objects/data_containers.py", line 3801, in _generate_field self.pf.field_info[field].check_available(self) File "/home/skillman/local/src/yt-hg/yt/data_objects/field_info_container.py", line 364, in check_available validator(data) File "/home/skillman/local/src/yt-hg/yt/data_objects/field_info_container.py", line 494, in __call__ raise NeedsGridType(self.ghost_zones,self.fields) yt.data_objects.field_info_container.NeedsGridType: (1, ['x-velocity', 'y-velocity', 'z-velocity']) ``` We should catch this and report back to the user to require the correct number of ghost zones Responsible: samskillman -- 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