Dear yt:
I was able to match my input data with the domain_dimension but still I am
getting an error as below. The link to files are below. Wherein
Expl_B_n.mtx is the original file whereas split1.txt is the file that
matches domain_dimension.
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Error:-
Traceback (most recent call last):
File "numpy_loadtxt.py", line 31, in <module>
slc = yt.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)
Thank you in advance
On Tue, Jan 12, 2016 at 10:04 AM, <yt-users-request@lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Re: Error while using SlicePlot (Nathan Goldbaum)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 12 Jan 2016 10:03:41 -0600
> From: Nathan Goldbaum <nathan12343@gmail.com>
> To: Discussion of the yt analysis package
> <yt-users@lists.spacepope.org>
> Subject: Re: [yt-users] Error while using SlicePlot
> Message-ID:
> <
> CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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@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@lists.spacepope.org>
> > wrote:
> >
> >> Send yt-users mailing list submissions to
> >> yt-users@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@lists.spacepope.org
> >>
> >> You can reach the person managing the list at
> >> yt-users-owner@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: Error while using SlicePlot (Nathan Goldbaum)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Mon, 11 Jan 2016 16:27:17 -0600
> >> From: Nathan Goldbaum <nathan12343@gmail.com>
> >> To: Discussion of the yt analysis package
> >> <yt-users@lists.spacepope.org>
> >> Subject: Re: [yt-users] Error while using SlicePlot
> >> Message-ID:
> >> <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd=
> >> LZdbzcHZg@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@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@lists.spacepope.org>
> >> > wrote:
> >> >
> >> >> Send yt-users mailing list submissions to
> >> >> yt-users@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@lists.spacepope.org
> >> >>
> >> >> You can reach the person managing the list at
> >> >> yt-users-owner@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@gmail.com>
> >> >> To: Discussion of the yt analysis package
> >> >> <yt-users@lists.spacepope.org>
> >> >> Subject: Re: [yt-users] Issue with loading data
> >> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667@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@cfa.harvard.edu
> >> >> jzuhone@gmail.com
> >> >> http://www.jzuhone.com
> >> >>
> >> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar <
> sushil.sush19us@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@lists.spacepope.org>
> >> >> wrote:
> >> >> >> Send yt-users mailing list submissions to
> >> >> >> yt-users@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@lists.spacepope.org
> >> >> >>
> >> >> >> You can reach the person managing the list at
> >> >> >> yt-users-owner@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@gmail.com>
> >> >> >> To: Discussion of the yt analysis package
> >> >> >> <yt-users@lists.spacepope.org>
> >> >> >> Subject: Re: [yt-users] problem with yt update to 3.0
> >> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022@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@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@gmail.com <mailto:sushil.sush19us@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@gmail.com>
> >> >> >> > Sent: Saturday, December 26, 2015 12:34 PM
> >> >> >> > To: Sushilkumar <mailto:sushil.sush19us@gmail.com>
> >> >> >> > Cc: Discussion of the yt analysis package <mailto:
> >> >> yt-users@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@gmail.com <mailto:sushil.sush19us@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@gmail.com
> >> >> <mailto:nathan12343@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@gmail.com <mailto:sushil.sush19us@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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:sushil.sush19us@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@lists.spacepope.org <mailto:
> >> >> yt-users-request@lists.spacepope.org>> wrote:
> >> >> >> >
> >> >> >> > Send yt-users mailing list submissions to
> >> >> >> > yt-users@lists.spacepope.org <mailto:
> >> >> yt-users@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@lists.spacepope.org <mailto:
> >> >> yt-users-request@lists.spacepope.org>
> >> >> >> >
> >> >> >> > You can reach the person managing the list at
> >> >> >> > yt-users-owner@lists.spacepope.org <mailto:
> >> >> yt-users-owner@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@gmail.com <mailto:
> >> >> nathan12343@gmail.com>>
> >> >> >> > To: Discussion of the yt analysis package
> >> >> >> > <yt-users@lists.spacepope.org <mailto:
> >> >> yt-users@lists.spacepope.org>>
> >> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary
> volumes
> >> >> >> > Message-ID:
> >> >> >> > <
> >> >> CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com
> >> >> <mailto:
> >> >> CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@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@gmail.com
> >> >> <mailto:bwoshea@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@gmail.com
> >> >> <mailto:bwoshea@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@gmail.com <mailto:nathan12343@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@gmail.com
> >> >> <mailto:bwoshea@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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:nathan12343@gmail.com>>
> >> wrote:
> >> >> >> > >>>>>
> >> >> >> > >>>>>>
> >> >> >> > >>>>>>
> >> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <
> >> >> bwoshea@gmail.com <mailto:bwoshea@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@lists.spacepope.org <mailto:
> >> >> yt-users@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
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> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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> >> >> >> > >>>>>
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> >> >> >> > >>>>
> >> >> >> > >>>> _______________________________________________
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> >> >> >> > >>>
> >> >> >> > >>
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> >> >>
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> >> >> >>
> >> >> >> >
> >> >> >> > ------------------------------
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> >> >> >> > Subject: Digest Footer
> >> >> >> >
> >> >> >> > _______________________________________________
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> >> >> >> >
> >> >> >> > ------------------------------
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> >> >> >> > 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@lists.spacepope.org <mailto:
> yt-users@lists.spacepope.org
> >> >
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> <
> >> >> 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
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> yt-users@lists.spacepope.org
> >> >
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> >> >> >
> >> >> >>
> >> >> >> ------------------------------
> >> >> >>
> >> >> >> Subject: Digest Footer
> >> >> >>
> >> >> >> _______________________________________________
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> >> >> >>
> >> >> >>
> >> >> >> ------------------------------
> >> >> >>
> >> >> >> 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
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> >> >> >
> >> >>
> >> >> ------------------------------
> >> >>
> >> >> Subject: Digest Footer
> >> >>
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> >> >>
> >> >> ------------------------------
> >> >>
> >> >> 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
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> >>
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> >>
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> >>
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> >>
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> >> ------------------------------
> >>
> >> 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@lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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>
--
*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.**"*
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Hi Sushil, I've looked at your data and script, and I think I see what's going on, but I need your help figuring out where to go from here. It looks to me like you have 1536 values, which correspond to 3 values for each cell in an 8x8x8 grid. I've rewritten your script slightly but don't know if I've done it correctly. This makes a dataset with 3 fields (field1, field2, field3 as I've called them) that is 8x8x8, and it slices them. Can you tell me if I am interpreting this correctly? Here is my modified version of the script: http://paste.yt-project.org/show/6144/ On Thu, Jan 14, 2016 at 11:08 AM, Sushilkumar <sushil.sush19us@gmail.com> wrote:
Dear yt:
I was able to match my input data with the domain_dimension but still I am getting an error as below. The link to files are below. Wherein Expl_B_n.mtx is the original file whereas split1.txt is the file that matches domain_dimension.
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Error:- Traceback (most recent call last): File "numpy_loadtxt.py", line 31, in <module> slc = yt.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)
Thank you in advance
On Tue, Jan 12, 2016 at 10:04 AM, <yt-users-request@lists.spacepope.org> wrote:
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Today's Topics:
1. Re: Error while using SlicePlot (Nathan Goldbaum)
----------------------------------------------------------------------
Message: 1 Date: Tue, 12 Jan 2016 10:03:41 -0600 From: Nathan Goldbaum <nathan12343@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] Error while using SlicePlot Message-ID:
<CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
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@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@lists.spacepope.org> wrote:
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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@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] Error while using SlicePlot Message-ID: <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= LZdbzcHZg@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@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
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@lists.spacepope.org> wrote:
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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@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] Issue with loading data Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667@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@cfa.harvard.edu jzuhone@gmail.com http://www.jzuhone.com
> On Jan 4, 2016, at 12:06 PM, Sushilkumar > <sushil.sush19us@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
"/state/partition1/anaconda/lib/python2.7/site-packages/yt/geometry/coordinates/cartesian_coordinates.py", link
below formats as numpy array but not from file. > >
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l...
> > > >> On Mon, Jan 4, 2016 at 10:52 AM, < yt-users-request@lists.spacepope.org> wrote: >> Send yt-users mailing list submissions to >> yt-users@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@lists.spacepope.org >> >> You can reach the person managing the list at >> yt-users-owner@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@gmail.com> >> To: Discussion of the yt analysis package >> <yt-users@lists.spacepope.org> >> Subject: Re: [yt-users] problem with yt update to 3.0 >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022@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-an...
<
http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-an...
> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < sushil.sush19us@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@gmail.com <mailto:sushil.sush19us@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@gmail.com> >> > Sent: Saturday, December 26, 2015 12:34 PM >> > To: Sushilkumar <mailto:sushil.sush19us@gmail.com> >> > Cc: Discussion of the yt analysis package <mailto: yt-users@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=l...
<
http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=l...
> >> > >> > >> > 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@gmail.com <mailto:sushil.sush19us@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@gmail.com <mailto:nathan12343@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/d9502d84802972ba3e644d2d5c47b87f73a...
<
> >> > >> > >> > 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@gmail.com <mailto:sushil.sush19us@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",
14, in <module> >> > File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py",
https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a... line 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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:sushil.sush19us@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-ve...
<
> >> > . >> > >> > 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@lists.spacepope.org <mailto: yt-users-request@lists.spacepope.org>> wrote: >> > >> > Send yt-users mailing list submissions to >> > yt-users@lists.spacepope.org <mailto: yt-users@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@lists.spacepope.org <mailto: yt-users-request@lists.spacepope.org> >> > >> > You can reach the person managing the list at >> > yt-users-owner@lists.spacepope.org <mailto: yt-users-owner@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@gmail.com <mailto: nathan12343@gmail.com>> >> > To: Discussion of the yt analysis package >> > <yt-users@lists.spacepope.org <mailto: yt-users@lists.spacepope.org>> >> > Subject: Re: [yt-users] problem with slices in non-unitary >> > volumes >> > Message-ID: >> > < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@mail.gmail.com <mailto:
CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@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@gmail.com <mailto:bwoshea@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
http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-ve... + + 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@gmail.com <mailto:bwoshea@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@gmail.com <mailto:nathan12343@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-creatin...
<
> >> > >>> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < bwoshea@gmail.com <mailto:bwoshea@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@gmail.com <mailto:nathan12343@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@gmail.com <mailto:nathan12343@gmail.com>> wrote: >> > >>>>> >> > >>>>>> >> > >>>>>> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < bwoshea@gmail.com <mailto:bwoshea@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
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
https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creatin... the 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@lists.spacepope.org <mailto: yt-users@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@lists.spacepope.org <mailto: yt-users@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@lists.spacepope.org <mailto: yt-users@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@lists.spacepope.org <mailto: yt-users@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@lists.spacepope.org <mailto: yt-users@lists.spacepope.org> >> > > >> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> > > >> >
participants (2)
-
Matthew Turk -
Sushilkumar