Dear yt: How do I write the fields to a file in the same format as my earlier split1.txt to check if the values are the same? On Thu, Jan 14, 2016 at 3:51 PM, <yt-users-request@lists.spacepope.org> wrote:
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1. Re: Error while using SlicePlot (Matthew Turk)
----------------------------------------------------------------------
Message: 1 Date: Thu, 14 Jan 2016 15:51:16 -0600 From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] Error while using SlicePlot Message-ID: <CALO3= 5GfJMK6C8Lp7xDWq-6LrL6y8TLk1oXOdFYdkAnJnpRkzg@mail.gmail.com> Content-Type: text/plain; charset=UTF-8
Hi Sushil,
You can change the order="C" to order="F". That ought to do it...
On Thu, Jan 14, 2016 at 3:50 PM, Sushilkumar <sushil.sush19us@gmail.com> wrote:
Dear yt:
Thank you Matthew Turk for helping with my script.
My original code is written in fortran. I think your code the fields are reshaped as per C. My original code output was of the form 1 column (x1,x2,x3,.....,y1,y2,y3,......z1,z2,z3), which need to be reshaped to (x1,y1,z1) . . . (xn,yn,zn)
How do I reshape the fields to to get desired output?
Thank you in advance
On Thu, Jan 14, 2016 at 2:01 PM, <yt-users-request@lists.spacepope.org> wrote:
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Today's Topics:
1. Re: Error while using SlicePlot (Matthew Turk)
----------------------------------------------------------------------
Message: 1 Date: Thu, 14 Jan 2016 14:01:37 -0600 From: Matthew Turk <matthewturk@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] Error while using SlicePlot Message-ID:
<CALO3=5GMCcT_YiqYsp5jT6Ot252fqEeSgLAMdzB7CuPaw-nKZg@mail.gmail.com> Content-Type: text/plain; charset=UTF-8
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,
I have no idea what the "correct" thing to do here is, but you'll to
so 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=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... > >> < > >> > > > 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", > 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-ve... > >> < > >> > > > 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 > 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... > >> < > >> > > > 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 > 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 > >> >> > >>>>> 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
> >> >> > > > >> >> > > > >> >> > -------------- next part -------------- > >> >> > An HTML attachment was scrubbed... > >> >> > URL: < > >> > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015... > >> < > >> > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015... > >> >> > >> >> > > >> >> > ------------------------------ > >> >> > > >> >> > Subject: Digest Footer > >> >> > > >> >> > _______________________________________________ > >> >> > 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
> >> >> > > >> >> > > >> >> > ------------------------------ > >> >> > > >> >> > 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 > > > >> >> > > >> >> > 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@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
> >> >> -------------- next part -------------- > >> >> An HTML attachment was scrubbed... > >> >> URL: < > >> > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2016... > >> > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users@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@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/2016... > >> > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users@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@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/2016... > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users@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.**"*
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End of yt-users Digest, Vol 95, Issue 13 ****************************************
-- 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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End of yt-users Digest, Vol 95, Issue 17 ****************************************
-- 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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End of yt-users Digest, Vol 95, Issue 19 ****************************************
-- *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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