[yt-users] Error while using SlicePlot

Nathan Goldbaum nathan12343 at gmail.com
Tue Jan 12 08:03:41 PST 2016


Hi,

The dimensions of your "vector" array need to match the domain_dimensions
you pass to load_uniform_grid. I was able to fake this by load_uniform_grid
the "arr" array of random numbers you generate in your script rather than
the data loaded in from the text file.

I'm not sure what the 1D vector in your u25.mtx file actually means, so I
have no idea what the "correct" thing to do here is, but you'll to pass in
data that has the same shape as the domain_dimensions you specify.

Admittedly, the error message you received was not very nice, so I've
opened a pull request to validate that the shapes of data passed to
load_uniform_grid are correct, and throw an error message if they are not.

Here is a sample script based on yours that runs without erroring out:

http://paste.yt-project.org/show/6140/

Hope that helps,

Nathan


On Mon, Jan 11, 2016 at 4:41 PM, Sushilkumar <sushil.sush19us at gmail.com>
wrote:

> Hi yt:
>
> Link to the Google drive is below. It has python script numpy_loadtxt.py
> and data set u25.mtx.
>
>
>
> https://drive.google.com/folderview?id=0B4g8shg4DL7oak5PLWVVdG5UMHc&usp=sharing
>
> On Mon, Jan 11, 2016 at 4:27 PM, <yt-users-request at lists.spacepope.org>
> wrote:
>
>> Send yt-users mailing list submissions to
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>> than "Re: Contents of yt-users digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Re: Error while using SlicePlot (Nathan Goldbaum)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 11 Jan 2016 16:27:17 -0600
>> From: Nathan Goldbaum <nathan12343 at gmail.com>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] Error while using SlicePlot
>> Message-ID:
>>         <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd=
>> LZdbzcHZg at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi Sushilkumar,
>>
>> Is there any chance you can share your full script, along with a sample
>> dataset that triggers the error? You can share the dataset using e.g.
>> dropbox or google drive.
>>
>> Thanks!
>>
>> -Nathan
>>
>> On Mon, Jan 11, 2016 at 4:25 PM, Sushilkumar <sushil.sush19us at gmail.com>
>> wrote:
>>
>> > Dear yt:
>> >
>> > Could you help me with the error below? It arises after using SlicePlot
>> > after formatting the data to numpy array from a file
>> >
>> >
>> > Traceback (most recent call last):
>> >   File "numpy_loadtxt.py", line 20, in <module>
>> >     slc = SlicePlot(pf, 2, ["Density"])
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
>> > line 2133, in SlicePlot
>> >     return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
>> > line 1274, in __init__
>> >     window_size=window_size, aspect=aspect)
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
>> > line 669, in __init__
>> >     PlotWindow.__init__(self, *args, **kwargs)
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
>> > line 249, in __init__
>> >     self._setup_plots()
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py",
>> > line 769, in _setup_plots
>> >     image = self.frb[f]
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/fixed_resolution.py",
>> > line 137, in __getitem__
>> >     int(self.antialias))
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/geometry/coordinates/cartesian_coordinates.py",
>> > line 57, in pixelize
>> >     antialias, dimension, periodic)
>> >   File
>> >
>> "/state/partition1/anaconda/lib/python2.7/site-packages/yt/geometry/coordinates/cartesian_coordinates.py",
>> > line 74, in _ortho_pixelize
>> >     period, int(periodic)).transpose()
>> > _MPL.error: data is of incorrect type (wanted 1D float)
>> >
>> >
>> >
>> > On Mon, Jan 4, 2016 at 11:10 AM, <yt-users-request at lists.spacepope.org>
>> > wrote:
>> >
>> >> Send yt-users mailing list submissions to
>> >>         yt-users at lists.spacepope.org
>> >>
>> >> To subscribe or unsubscribe via the World Wide Web, visit
>> >>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> or, via email, send a message with subject or body 'help' to
>> >>         yt-users-request at lists.spacepope.org
>> >>
>> >> You can reach the person managing the list at
>> >>         yt-users-owner at lists.spacepope.org
>> >>
>> >> When replying, please edit your Subject line so it is more specific
>> >> than "Re: Contents of yt-users digest..."
>> >>
>> >>
>> >> Today's Topics:
>> >>
>> >>    1. Re: Issue with loading data (John ZuHone)
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Mon, 4 Jan 2016 12:10:11 -0500
>> >> From: John ZuHone <jzuhone at gmail.com>
>> >> To: Discussion of the yt analysis package
>> >>         <yt-users at lists.spacepope.org>
>> >> Subject: Re: [yt-users] Issue with loading data
>> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667 at gmail.com>
>> >> Content-Type: text/plain; charset="utf-8"
>> >>
>> >> yt.loadtxt only works in the current development version of the 3.x
>> >> series of yt.
>> >>
>> >> John ZuHone
>> >> Harvard-Smithsonian Center for Astrophysics
>> >>
>> >> 60 Garden St., MS-67
>> >> Cambridge, MA 02138
>> >> (w) 617-496-1816
>> >> (m) 781-708-5004
>> >> jzuhone at cfa.harvard.edu
>> >> jzuhone at gmail.com
>> >> http://www.jzuhone.com
>> >>
>> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar <sushil.sush19us at gmail.com>
>> >> wrote:
>> >> >
>> >> > Dear yt:
>> >> >
>> >> > Can I use yt.loadtxt for yt version 2.6.1?
>> >> > Are there examples for "loading from file" using numpy array? The
>> link
>> >> below formats as numpy array but not from file.
>> >> >
>> >> >
>> >>
>> http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
>> >> >
>> >> >
>> >> >
>> >> >> On Mon, Jan 4, 2016 at 10:52 AM, <
>> yt-users-request at lists.spacepope.org>
>> >> wrote:
>> >> >> Send yt-users mailing list submissions to
>> >> >>         yt-users at lists.spacepope.org
>> >> >>
>> >> >> To subscribe or unsubscribe via the World Wide Web, visit
>> >> >>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >> or, via email, send a message with subject or body 'help' to
>> >> >>         yt-users-request at lists.spacepope.org
>> >> >>
>> >> >> You can reach the person managing the list at
>> >> >>         yt-users-owner at lists.spacepope.org
>> >> >>
>> >> >> When replying, please edit your Subject line so it is more specific
>> >> >> than "Re: Contents of yt-users digest..."
>> >> >>
>> >> >>
>> >> >> Today's Topics:
>> >> >>
>> >> >>    1. Re: problem with yt update to 3.0 (John ZuHone)
>> >> >>
>> >> >>
>> >> >>
>> ----------------------------------------------------------------------
>> >> >>
>> >> >> Message: 1
>> >> >> Date: Mon, 4 Jan 2016 11:52:03 -0500
>> >> >> From: John ZuHone <jzuhone at gmail.com>
>> >> >> To: Discussion of the yt analysis package
>> >> >>         <yt-users at lists.spacepope.org>
>> >> >> Subject: Re: [yt-users] problem with yt update to 3.0
>> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022 at gmail.com>
>> >> >> Content-Type: text/plain; charset="utf-8"
>> >> >>
>> >> >> In the current development version of yt there is also yt.loadtxt,
>> >> which is essentially a wrapper for numpy.loadtxt which also accepts
>> unit
>> >> information.
>> >> >>
>> >> >> See
>> >>
>> http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk
>> >> <
>> >>
>> http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk
>> >> >
>> >> >>
>> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar <
>> sushil.sush19us at gmail.com>
>> >> wrote:
>> >> >> >
>> >> >> > Dear Nathan:
>> >> >> >
>> >> >> > As per your advice I am trying to load my text file to numpy
>> array.
>> >> But there are two ways to so using numpy.loadtxt and numpy.fromfile.
>> Could
>> >> you suggest which of them is more efficient for large files and more
>> >> suitable for yt (if any)?
>> >> >> >
>> >> >> > Thanks in advance
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar <
>> >> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> >> >> > Dear Nathan:
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > Thank you for your help
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > SK2
>> >> >> >
>> >> >> > "Claiming that something can move faster than light is a good
>> >> conversation-stopper in physics. People edge away from you in cocktail
>> >> parties; friends never return phone calls. You just don?t mess with
>> Albert
>> >> Einstein."
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > From: Nathan Goldbaum <mailto:nathan12343 at gmail.com>
>> >> >> > Sent: Saturday, December 26, 2015 12:34 PM
>> >> >> > To: Sushilkumar <mailto:sushil.sush19us at gmail.com>
>> >> >> > Cc: Discussion of the yt analysis package <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> > Subject: Re: [yt-users] problem with yt update to 3.0
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > If you can format your data as numpy arrays, there are examples of
>> >> how to load your data into yt here:
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >>
>> http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
>> >> <
>> >>
>> http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
>> >> >
>> >> >> >
>> >> >> >
>> >> >> > yt (2.6.1 or newer) does not support i/o from arbitrary text
>> files.
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar <
>> >> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> >> >> >
>> >> >> > Dear Nathan:
>> >> >> >
>> >> >> > I will try it and let you know. In the meanwhile, could you let me
>> >> know if yt supports loading text file for version 2.6.1? If so could
>> you
>> >> point me to examples for the same.
>> >> >> >
>> >> >> > Thanks in advance
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <
>> nathan12343 at gmail.com
>> >> <mailto:nathan12343 at gmail.com>> wrote:
>> >> >> >
>> >> >> > This is happening because python is unable to link against an
>> >> openSSL library.
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > Can you try using the get_yt.sh script install of the
>> >> install_script.sh script:
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >>
>> https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh
>> >> <
>> >>
>> https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh
>> >> >
>> >> >> >
>> >> >> >
>> >> >> > This script installs yt using the miniconda python distribution,
>> >> which includes a precompiled python and openSSL library.
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > -Nathan
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar <
>> >> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> >> >> >
>> >> >> > Hi Nathan:
>> >> >> >
>> >> >> > Thanks for your reply.
>> >> >> >
>> >> >> > I had  done that before installing version 2.X. I used to get
>> errors
>> >> as below. Even now I keep getting the same error after reinstalling
>> from
>> >> scratch. The error comes after "installing pip". I tried it on my pc
>> and
>> >> also on cluster but same issues.
>> >> >> >
>> >> >> > ********************************************
>> >> >> >         FAILURE REPORT:
>> >> >> > ********************************************
>> >> >> >
>> >> >> >     bootstrap(tmpdir=tmpdir)
>> >> >> >   File "get-pip.py", line 82, in bootstrap
>> >> >> >     import pip
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in
>> <module>
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in
>> >> <module>
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module>
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module>
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py",
>> line
>> >> 14, in <module>
>> >> >> >   File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py",
>> line
>> >> 31, in <module>
>> >> >> > ImportError: cannot import name HTTPSHandler
>> >> >> >
>> >> >> > ********************************************
>> >> >> > ********************************************
>> >> >> > Failure.  Check /home/adrith/yt-x86_64/yt_install.log.  The last
>> 10
>> >> lines are above.
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum <
>> >> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
>> >> >> >
>> >> >> > Hi Sushilkumar,
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > Can you try reinstalling yt from scratch?
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > -Nathan
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <
>> >> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
>> >> >> >
>> >> >> > Dear yt:
>> >> >> >
>> >> >> > I am currently running yt version 2.6.1 and want to update to
>> >> version 3 (to read text files). Could you provide me link to so?
>> >> >> >
>> >> >> > I tried it using yt update --all as per the link
>> >> >> >
>> >> >> >
>> >>
>> http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back
>> >> <
>> >>
>> http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back
>> >> >
>> >> >> > .
>> >> >> >
>> >> >> > But it wont update to 3.0 and still shows as 2.6.1
>> >> >> >
>> >> >> > Kindly help
>> >> >> >
>> >> >> > Thanks in advance
>> >> >> >
>> >> >> > sushilkumar
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Thu, Dec 24, 2015 at 12:25 PM, <
>> >> yt-users-request at lists.spacepope.org <mailto:
>> >> yt-users-request at lists.spacepope.org>> wrote:
>> >> >> >
>> >> >> > Send yt-users mailing list submissions to
>> >> >> >         yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> >
>> >> >> > To subscribe or unsubscribe via the World Wide Web, visit
>> >> >> >
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > or, via email, send a message with subject or body 'help' to
>> >> >> >         yt-users-request at lists.spacepope.org <mailto:
>> >> yt-users-request at lists.spacepope.org>
>> >> >> >
>> >> >> > You can reach the person managing the list at
>> >> >> >         yt-users-owner at lists.spacepope.org <mailto:
>> >> yt-users-owner at lists.spacepope.org>
>> >> >> >
>> >> >> > When replying, please edit your Subject line so it is more
>> specific
>> >> >> > than "Re: Contents of yt-users digest..."
>> >> >> >
>> >> >> >
>> >> >> > Today's Topics:
>> >> >> >
>> >> >> >    1. Re: problem with slices in non-unitary volumes (Nathan
>> >> Goldbaum)
>> >> >> >
>> >> >> >
>> >> >> >
>> >> ----------------------------------------------------------------------
>> >> >> >
>> >> >> > Message: 1
>> >> >> > Date: Wed, 23 Dec 2015 17:17:56 -0600
>> >> >> > From: Nathan Goldbaum <nathan12343 at gmail.com <mailto:
>> >> nathan12343 at gmail.com>>
>> >> >> > To: Discussion of the yt analysis package
>> >> >> >         <yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>>
>> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary volumes
>> >> >> > Message-ID:
>> >> >> >         <
>> >> CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g at mail.gmail.com
>> >> <mailto:
>> >> CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g at mail.gmail.com>>
>> >> >> > Content-Type: text/plain; charset="utf-8"
>> >> >> >
>> >> >> > I get the same error over here. I think it's unrelated to the
>> other
>> >> error.
>> >> >> > The relevant portion of the C stack trace is here:
>> >> >> >
>> >> >> > Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
>> >> >> > 0   libsystem_kernel.dylib         0x00007fff8b615286
>> __pthread_kill
>> >> + 10
>> >> >> > 1   libsystem_c.dylib             0x00007fff8bc2a9ab abort + 129
>> >> >> > 2   libsystem_malloc.dylib         0x00007fff915d5fe2 szone_error
>> +
>> >> 625
>> >> >> > 3   libsystem_malloc.dylib         0x00007fff915cf374
>> >> >> > small_free_list_remove_ptr + 154
>> >> >> > 4   libsystem_malloc.dylib         0x00007fff915cac3f
>> >> >> > szone_free_definite_size + 1856
>> >> >> > 5   multiarray.so                 0x00000001044c2d16
>> npy_free_cache
>> >> + 70
>> >> >> > 6   multiarray.so                 0x00000001044c6ed6
>> array_dealloc +
>> >> 182
>> >> >> > 7   selection_routines.so         0x00000001063ffe34
>> >> >> >
>> >> __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask
>> +
>> >> >> > 8804 (selection_routines.c:19749)
>> >> >> >
>> >> >> > Line 19749 of selection_routines.c corresponds to line 1158 in
>> >> >> > selection_routines.pyx, which is the place where the fill_mask
>> member
>> >> >> > variable of the SliceSelector extension type gets defined.
>> >> >> >
>> >> >> > Unfortunately, I have no idea how to debug this from here...
>> >> >> >
>> >> >> > -Nathan
>> >> >> >
>> >> >> > On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <bwoshea at gmail.com
>> >> <mailto:bwoshea at gmail.com>> wrote:
>> >> >> >
>> >> >> > > Actually, interesting followup here - I have to take it back.
>> >> When I do a
>> >> >> > > projection plot:
>> >> >> > >
>> >> >> > >     yt.ProjectionPlot(ds,'x',("gas",
>> >> >> > > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
>> >> >> > >
>> >> >> > > the behavior is perfectly fine and I get projections that look
>> >> sensible.
>> >> >> > >  *however*, when I do a slice plot:
>> >> >> > >
>> >> >> > >    yt.SlicePlot(ds,'x',("gas",
>> >> >> > > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
>> >> >> > >
>> >> >> > > I get a malloc error:
>> >> >> > >
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,082 Gathering a field list
>> >> (this may
>> >> >> > > take a moment.)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,155 Loading field plugins.
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,155 Loaded angular_momentum
>> >> (8 new
>> >> >> > > fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded astro (16 new
>> >> fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded cosmology (23
>> new
>> >> fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,156 Loaded fluid (64 new
>> >> fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96
>> >> new
>> >> >> > > fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded geometric (112
>> new
>> >> fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded local (112 new
>> >> fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,157 Loaded magnetic_field
>> >> (120 new
>> >> >> > > fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,158 Loaded my_plugins (120
>> >> new fields)
>> >> >> > > yt : [INFO     ] 2015-12-23 17:50:59,158 Loaded species (122 new
>> >> fields)
>> >> >> > > python2.7(12254,0x7fff72d19310) malloc: *** error for object
>> >> 0x103e39008:
>> >> >> > > incorrect checksum for freed object - object was probably
>> modified
>> >> after
>> >> >> > > being freed.
>> >> >> > > *** set a breakpoint in malloc_error_break to debug
>> >> >> > > Abort trap: 6
>> >> >> > >
>> >> >> > > This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my
>> >> Linux
>> >> >> > > machine (Ubuntu 13.04, gcc 4.6.3), although on the linux
>> machine I
>> >> just get
>> >> >> > > a seg fault instead of the malloc stuff.  Using pdb (python -m
>> pdb
>> >> >> > > crashing_script.py) gives me the same error with no additional
>> >> information.
>> >> >> > >
>> >> >> > >
>> >> >> > > On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <
>> bwoshea at gmail.com
>> >> <mailto:bwoshea at gmail.com>> wrote:
>> >> >> > >
>> >> >> > >> Bugfix confirmed; this works for me as well.  Thank you very
>> much!
>> >> >> > >>
>> >> >> > >> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
>> >> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>>
>> >> >> > >> wrote:
>> >> >> > >>
>> >> >> > >>> I've opened a pull request that allows me to load your
>> dataset:
>> >> >> > >>>
>> >> >> > >>>
>> >> >> > >>>
>> >>
>> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
>> >> <
>> >>
>> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
>> >> >
>> >> >> > >>>
>> >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <
>> bwoshea at gmail.com
>> >> <mailto:bwoshea at gmail.com>> wrote:
>> >> >> > >>>
>> >> >> > >>>> Oh, interesting.  Is there a way to circumvent auto-detection
>> >> of fields?
>> >> >> > >>>>
>> >> >> > >>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
>> >> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>
>> >> >> > >>>> > wrote:
>> >> >> > >>>>
>> >> >> > >>>>> It looks like field detection is breaking for this Enzo-3.0
>> >> active
>> >> >> > >>>>> particle dataset. StoredEnergy is available on-disk as
>> >> ('AGNParticle,
>> >> >> > >>>>> 'StoredEnergy'), but for some reason the field detection
>> >> system isn't able
>> >> >> > >>>>> to guess that.
>> >> >> > >>>>>
>> >> >> > >>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <
>> >> >> > >>>>> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>>
>> wrote:
>> >> >> > >>>>>
>> >> >> > >>>>>>
>> >> >> > >>>>>>
>> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <
>> >> bwoshea at gmail.com <mailto:bwoshea at gmail.com>>
>> >> >> > >>>>>> wrote:
>> >> >> > >>>>>>
>> >> >> > >>>>>>> Dear yt-users,
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> I'm having a problem with making slices in non-unitary
>> >> volumes.  I
>> >> >> > >>>>>>> have a 3D enzo simulation that has domain bounds of
>> >> (-1.6...1.6) in every
>> >> >> > >>>>>>> dimension (units of megaparsecs), and after I updated to
>> the
>> >> tip of yt-3
>> >> >> > >>>>>>> (changeset d9502d848029) from a fairly old version of the
>> >> code I suddenly
>> >> >> > >>>>>>> have problems with making simple projections.  If I run
>> this
>> >> set of
>> >> >> > >>>>>>> commands:
>> >> >> > >>>>>>>
>> >> >> > >>>>>>>
>> >> >> > >>>>>> Any idea which version you updated from? I tried on yt-3.1
>> >> and get
>> >> >> > >>>>>> the same error. This is just so we can bisect and find the
>> >> change that
>> >> >> > >>>>>> introduced the regression.
>> >> >> > >>>>>>
>> >> >> > >>>>>>
>> >> >> > >>>>>>> import yt
>> >> >> > >>>>>>> ds = yt.load("DD0400/DD0400")
>> >> >> > >>>>>>> proj =
>> >> >> > >>>>>>>
>> >>
>> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> I get this error:
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> http://paste.yt-project.org/show/6115/ <
>> >> http://paste.yt-project.org/show/6115/>
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> This seems to work fine on an Enzo cosmological dataset
>> >> (domain
>> >> >> > >>>>>>> bounds 0-1 in each dimension), and previously worked fine
>> in
>> >> yt-3 (using a
>> >> >> > >>>>>>> version of the code from a couple of months ago).
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> is this a bug, or am I doing something dumb?
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> Thanks!
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> --Brian
>> >> >> > >>>>>>>
>> >> >> > >>>>>>>
>> >> >> > >>>>>>> _______________________________________________
>> >> >> > >>>>>>> yt-users mailing list
>> >> >> > >>>>>>> yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> > >>>>>>>
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > >>>>>>>
>> >> >> > >>>>>>>
>> >> >> > >>>>>>
>> >> >> > >>>>>
>> >> >> > >>>>> _______________________________________________
>> >> >> > >>>>> yt-users mailing list
>> >> >> > >>>>> yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> > >>>>>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > >>>>>
>> >> >> > >>>>>
>> >> >> > >>>>
>> >> >> > >>>> _______________________________________________
>> >> >> > >>>> yt-users mailing list
>> >> >> > >>>> yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> > >>>>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > >>>>
>> >> >> > >>>>
>> >> >> > >>>
>> >> >> > >>> _______________________________________________
>> >> >> > >>> yt-users mailing list
>> >> >> > >>> yt-users at lists.spacepope.org <mailto:
>> >> yt-users at lists.spacepope.org>
>> >> >> > >>>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > >>>
>> >> >> > >>>
>> >> >> > >>
>> >> >> > >
>> >> >> > > _______________________________________________
>> >> >> > > yt-users mailing list
>> >> >> > > yt-users at lists.spacepope.org <mailto:
>> yt-users at lists.spacepope.org>
>> >> >> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> > >
>> >> >> > >
>> >> >> > -------------- next part --------------
>> >> >> > An HTML attachment was scrubbed...
>> >> >> > URL: <
>> >>
>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151223/0739ada6/attachment.html
>> >> <
>> >>
>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151223/0739ada6/attachment.html
>> >> >>
>> >> >> >
>> >> >> > ------------------------------
>> >> >> >
>> >> >> > Subject: Digest Footer
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > yt-users mailing list
>> >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
>> >
>> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------
>> >> >> >
>> >> >> > End of yt-users Digest, Vol 94, Issue 24
>> >> >> > ****************************************
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> >
>> >> >> > SK2
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > "Claiming that something can move faster than light is a good
>> >> conversation-stopper in physics. People edge away from you in cocktail
>> >> parties; friends never return phone calls. You just don?t mess with
>> Albert
>> >> Einstein."
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > yt-users mailing list
>> >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
>> >
>> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> >
>> >> >> > SK2
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > "Claiming that something can move faster than light is a good
>> >> conversation-stopper in physics. People edge away from you in cocktail
>> >> parties; friends never return phone calls. You just don?t mess with
>> Albert
>> >> Einstein."
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > SK2
>> >> >> >
>> >> >> > "Claiming that something can move faster than light is a good
>> >> conversation-stopper in physics. People edge away from you in cocktail
>> >> parties; friends never return phone calls. You just don?t mess with
>> Albert
>> >> Einstein."
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > yt-users mailing list
>> >> >> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org
>> >
>> >> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
>> >> >> -------------- next part --------------
>> >> >> An HTML attachment was scrubbed...
>> >> >> URL: <
>> >>
>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160104/e649ce9b/attachment.htm
>> >> >
>> >> >>
>> >> >> ------------------------------
>> >> >>
>> >> >> Subject: Digest Footer
>> >> >>
>> >> >> _______________________________________________
>> >> >> yt-users mailing list
>> >> >> yt-users at lists.spacepope.org
>> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> >>
>> >> >>
>> >> >> ------------------------------
>> >> >>
>> >> >> End of yt-users Digest, Vol 95, Issue 2
>> >> >> ***************************************
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > SK2
>> >> >
>> >> > "Claiming that something can move faster than light is a good
>> >> conversation-stopper in physics. People edge away from you in cocktail
>> >> parties; friends never return phone calls. You just don?t mess with
>> Albert
>> >> Einstein."
>> >> >
>> >> > _______________________________________________
>> >> > yt-users mailing list
>> >> > yt-users at lists.spacepope.org
>> >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >> -------------- next part --------------
>> >> An HTML attachment was scrubbed...
>> >> URL: <
>> >>
>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160104/36f5165e/attachment.htm
>> >> >
>> >>
>> >> ------------------------------
>> >>
>> >> Subject: Digest Footer
>> >>
>> >> _______________________________________________
>> >> yt-users mailing list
>> >> yt-users at lists.spacepope.org
>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> End of yt-users Digest, Vol 95, Issue 4
>> >> ***************************************
>> >>
>> >
>> >
>> >
>> > --
>> > *SK2*
>> >
>> > *"**Claiming that something can move faster than light is a good
>> > conversation-stopper in physics. People edge away from you in cocktail
>> > parties; friends never return phone calls. You just don?t mess with
>> Albert
>> > Einstein.**"*
>> >
>> >
>> > _______________________________________________
>> > yt-users mailing list
>> > yt-users at lists.spacepope.org
>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >
>> >
>> -------------- next part --------------
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>> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160111/d9f8f8d6/attachment.htm
>> >
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>> ------------------------------
>>
>> End of yt-users Digest, Vol 95, Issue 11
>> ****************************************
>>
>
>
>
> --
> *SK2*
>
> *"**Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don’t mess with Albert
> Einstein.**"*
>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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