Mailman 3 April 2013 - yt-dev

[yt_analysis/yt] Athena object storage (issue #540)
by Sam Skillman 02 Apr '13

02 Apr '13

New issue 540: Athena object storage https://bitbucket.org/yt_analysis/yt/issue/540/athena-object-storage Sam Skillman: Athena object storage should be implemented by setting up the correct storage location. Currently there is just a pass in the specialized initialize_object_storage function. This was probably an oversight by me a while back. 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.

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[yt_analysis/yt] h5py serialization (issue #539)
by Sam Skillman 02 Apr '13

02 Apr '13

New issue 539: h5py serialization https://bitbucket.org/yt_analysis/yt/issue/539/h5py-serialization Sam Skillman: It seems that with some version of h5py, we now run into these issues when using pf.h.save_object() with any type of data: ``` #!python In [1]: pf.h.save_object(np.ones(10), 'ones') /home/skillman/local/lib/python2.7/site-packages/h5py/_hl/dataset.py:94: RuntimeWarning: tp_compare didn't return -1 or -2 for exception dset_id.write(h5s.ALL, h5s.ALL, data) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/skillman/local/src/yt-hg/yt/mods.pyc in <module>() ----> 1 pf.h.save_object(np.ones(10), 'ones') /home/skillman/local/src/yt-hg/yt/data_objects/hierarchy.pyc in save_object(self, obj, name) 318 """ 319 s = cPickle.dumps(obj, protocol=-1) --> 320 self.save_data(s, "/Objects", name, force = True) 321 322 def load_object(self, name): /home/skillman/local/src/yt-hg/yt/data_objects/hierarchy.pyc in _save_data(self, array, node, name, set_attr, force, passthrough) 293 for q in node.split('/'): 294 if q: myGroup = myGroup.require_group(q) --> 295 arr = myGroup.create_dataset(name,data=array) 296 if set_attr is not None: 297 for i, j in set_attr.items(): arr.attrs[i] = j /home/skillman/local/lib/python2.7/site-packages/h5py/_hl/group.pyc in create_dataset(self, name, shape, dtype, data, **kwds) 69 """ 70 ---> 71 dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) 72 dset = dataset.Dataset(dsid) 73 if name is not None: /home/skillman/local/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue) 92 93 if data is not None: ---> 94 dset_id.write(h5s.ALL, h5s.ALL, data) 95 96 return dset_id /home/skillman/local/lib/python2.7/site-packages/h5py/h5d.so in h5py.h5d.DatasetID.write (h5py/h5d.c:2866)() /home/skillman/local/lib/python2.7/site-packages/h5py/_proxy.so in h5py._proxy.dset_rw (h5py/_proxy.c:1766)() /home/skillman/local/lib/python2.7/site-packages/h5py/defs.so in h5py.defs.H5Tconvert (h5py/defs.c:18439)() /home/skillman/local/lib/python2.7/site-packages/h5py/_errors.so in h5py._errors.set_exception (h5py/_errors.c:711)() /home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.str2vlen (h5py/_conv.c:3382)() /home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.generic_converter (h5py/_conv.c:1302)() /home/skillman/local/lib/python2.7/site-packages/h5py/_conv.so in h5py._conv.conv_str2vlen (h5py/_conv.c:2158)() ValueError: VLEN strings do not support embedded NULLs In [2]: ``` 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.

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fixing particle information for the ellipsoid container
by Geoffrey So 02 Apr '13

02 Apr '13

Hi all, Currently the ellipsoid 3D container has a couple short coming that makes it undesirable to use, I think the most major one is that it does not return the particle information (positions, velocities, type etc) I am interested at least in fixing it, because I may use this directly in my research, so I was wondering if anyone has worked on 3D containers to help me out in digging for the cause of this? The code that describes the 3D container is in this file yt-hg/yt/data_objects/data_containers.py Originally, I emulated what was done with the sphere 3D object, and I thought I followed everything that was done, but obviously I missed something. It is possibly very subtle or glaringly visible but I am just blind to it. any thoughts or hints for what to look at/where to dig would be appreciated. From G.S.

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YTEP-0012: Halos
by Matthew Turk 01 Apr '13

01 Apr '13

Hi all, Britton issued a pull request for YTEP-0012, which covers halo finding, merger trees, and halo profiling. https://bitbucket.org/yt_analysis/ytep/pull-request/14/ytep-12-halo-analysi… I'm going to be leaving comments on it today, but if you are at all remotely interested in this functionality, I'd encourage you to submit feedback on it. -Matt

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