Mailman 3 January 2016 - yt-users

Error with SlicePlot
by Sushilkumar Jan. 14, 2016

Jan. 14, 2016

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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 (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Jan 2016 15:51:16 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using SlicePlot > Message-ID: > <CALO3= > 5GfJMK6C8Lp7xDWq-6LrL6y8TLk1oXOdFYdkAnJnpRkzg(a)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(a)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(a)lists.spacepope.org> > > wrote: > >> > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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 (Matthew Turk) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 14 Jan 2016 14:01:37 -0600 > >> From: Matthew Turk <matthewturk(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] Error while using SlicePlot > >> Message-ID: > >> > >> <CALO3=5GMCcT_YiqYsp5jT6Ot252fqEeSgLAMdzB7CuPaw-nKZg(a)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(a)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(a)lists.spacepope.org> > >> > wrote: > >> >> > >> >> Send yt-users mailing list submissions to > >> >> yt-users(a)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(a)lists.spacepope.org > >> >> > >> >> You can reach the person managing the list at > >> >> yt-users-owner(a)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: Tue, 12 Jan 2016 10:03:41 -0600 > >> >> From: Nathan Goldbaum <nathan12343(a)gmail.com> > >> >> To: Discussion of the yt analysis package > >> >> <yt-users(a)lists.spacepope.org> > >> >> Subject: Re: [yt-users] Error while using SlicePlot > >> >> Message-ID: > >> >> > >> >> <CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g(a)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(a)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=sha… > >> >> > > >> >> > On Mon, Jan 11, 2016 at 4:27 PM, > >> >> > <yt-users-request(a)lists.spacepope.org> > >> >> > wrote: > >> >> > > >> >> >> Send yt-users mailing list submissions to > >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> > >> >> >> You can reach the person managing the list at > >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> To: Discussion of the yt analysis package > >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> Subject: Re: [yt-users] Error while using SlicePlot > >> >> >> Message-ID: > >> >> >> <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= > >> >> >> LZdbzcHZg(a)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(a)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(a)lists.spacepope.org> > >> >> >> > wrote: > >> >> >> > > >> >> >> >> Send yt-users mailing list submissions to > >> >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> >> > >> >> >> >> You can reach the person managing the list at > >> >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> >> To: Discussion of the yt analysis package > >> >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> >> Subject: Re: [yt-users] Issue with loading data > >> >> >> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > >> >> >> >> jzuhone(a)gmail.com > >> >> >> >> http://www.jzuhone.com > >> >> >> >> > >> >> >> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar > >> >> >> >> > <sushil.sush19us(a)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=… > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> >> On Mon, Jan 4, 2016 at 10:52 AM, < > >> >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> >> wrote: > >> >> >> >> >> Send yt-users mailing list submissions to > >> >> >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> >> >> > >> >> >> >> >> You can reach the person managing the list at > >> >> >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> >> >> To: Discussion of the yt analysis package > >> >> >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> >> >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> >> >> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > >> >> >> >> > > >> >> >> >> >> > >> >> >> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < > >> >> >> sushil.sush19us(a)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(a)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(a)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=… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > 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(a)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(a)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(a)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-v… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > >> >> >> >> > > >> >> >> >> >> > . > >> >> >> >> >> > > >> >> >> >> >> > 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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-request(a)lists.spacepope.org>> wrote: > >> >> >> >> >> > > >> >> >> >> >> > Send yt-users mailing list submissions to > >> >> >> >> >> > yt-users(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> >> >> > > >> >> >> >> >> > You can reach the person managing the list at > >> >> >> >> >> > yt-users-owner(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-owner(a)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(a)gmail.com <mailto: > >> >> >> >> nathan12343(a)gmail.com>> > >> >> >> >> >> > To: Discussion of the yt analysis package > >> >> >> >> >> > <yt-users(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)lists.spacepope.org>> > >> >> >> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary > >> >> >> >> >> > volumes > >> >> >> >> >> > Message-ID: > >> >> >> >> >> > < > >> >> >> >> > >> >> >> >> > CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > >> >> >> >> <mailto: > >> >> >> >> > >> >> >> >> > >> >> >> >> > CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > >> >> >> >> > > >> >> >> >> >> > >>> > >> >> >> >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < > >> >> >> bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com > >> > >> >> >> wrote: > >> >> >> >> >> > >>>>> > >> >> >> >> >> > >>>>>> > >> >> >> >> >> > >>>>>> > >> >> >> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > >> >> >> >> bwoshea(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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/201… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> >> >> >> >> > >> >> >> >> >> > > >> >> >> >> >> > ------------------------------ > >> >> >> >> >> > > >> >> >> >> >> > Subject: Digest Footer > >> >> >> >> >> > > >> >> >> >> >> > _______________________________________________ > >> >> >> >> >> > yt-users mailing list > >> >> >> >> >> > yt-users(a)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(a)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(a)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/201… > >> >> >> >> > > >> >> >> >> >> > >> >> >> >> >> ------------------------------ > >> >> >> >> >> > >> >> >> >> >> Subject: Digest Footer > >> >> >> >> >> > >> >> >> >> >> _______________________________________________ > >> >> >> >> >> yt-users mailing list > >> >> >> >> >> yt-users(a)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(a)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/201… > >> >> >> >> > > >> >> >> >> > >> >> >> >> ------------------------------ > >> >> >> >> > >> >> >> >> Subject: Digest Footer > >> >> >> >> > >> >> >> >> _______________________________________________ > >> >> >> >> yt-users mailing list > >> >> >> >> yt-users(a)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(a)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/201… > >> >> >> > > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> Subject: Digest Footer > >> >> >> > >> >> >> _______________________________________________ > >> >> >> yt-users mailing list > >> >> >> yt-users(a)lists.spacepope.org > >> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> >> >> > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> End of yt-users Digest, Vol 95, Issue 11 > >> >> >> **************************************** > >> >> >> > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > *SK2* > >> >> > > >> >> > *"**Claiming that something can move faster than light is a good > >> >> > conversation-stopper in physics. People edge away from you in > >> >> > cocktail > >> >> > parties; friends never return phone calls. You just don?t mess with > >> >> > Albert > >> >> > Einstein.**"* > >> >> > > >> >> > > >> >> > _______________________________________________ > >> >> > yt-users mailing list > >> >> > yt-users(a)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/201… > > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users(a)lists.spacepope.org > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> >> > >> >> > >> >> ------------------------------ > >> >> > >> >> 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(a)lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> 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(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > 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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

1 0

Error with SlicePlot
by Sushilkumar Jan. 14, 2016

Jan. 14, 2016

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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 (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Jan 2016 15:51:16 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using SlicePlot > Message-ID: > <CALO3= > 5GfJMK6C8Lp7xDWq-6LrL6y8TLk1oXOdFYdkAnJnpRkzg(a)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(a)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(a)lists.spacepope.org> > > wrote: > >> > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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 (Matthew Turk) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 14 Jan 2016 14:01:37 -0600 > >> From: Matthew Turk <matthewturk(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] Error while using SlicePlot > >> Message-ID: > >> > >> <CALO3=5GMCcT_YiqYsp5jT6Ot252fqEeSgLAMdzB7CuPaw-nKZg(a)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(a)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(a)lists.spacepope.org> > >> > wrote: > >> >> > >> >> Send yt-users mailing list submissions to > >> >> yt-users(a)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(a)lists.spacepope.org > >> >> > >> >> You can reach the person managing the list at > >> >> yt-users-owner(a)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: Tue, 12 Jan 2016 10:03:41 -0600 > >> >> From: Nathan Goldbaum <nathan12343(a)gmail.com> > >> >> To: Discussion of the yt analysis package > >> >> <yt-users(a)lists.spacepope.org> > >> >> Subject: Re: [yt-users] Error while using SlicePlot > >> >> Message-ID: > >> >> > >> >> <CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g(a)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(a)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=sha… > >> >> > > >> >> > On Mon, Jan 11, 2016 at 4:27 PM, > >> >> > <yt-users-request(a)lists.spacepope.org> > >> >> > wrote: > >> >> > > >> >> >> Send yt-users mailing list submissions to > >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> > >> >> >> You can reach the person managing the list at > >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> To: Discussion of the yt analysis package > >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> Subject: Re: [yt-users] Error while using SlicePlot > >> >> >> Message-ID: > >> >> >> <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= > >> >> >> LZdbzcHZg(a)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(a)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(a)lists.spacepope.org> > >> >> >> > wrote: > >> >> >> > > >> >> >> >> Send yt-users mailing list submissions to > >> >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> >> > >> >> >> >> You can reach the person managing the list at > >> >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> >> To: Discussion of the yt analysis package > >> >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> >> Subject: Re: [yt-users] Issue with loading data > >> >> >> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > >> >> >> >> jzuhone(a)gmail.com > >> >> >> >> http://www.jzuhone.com > >> >> >> >> > >> >> >> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar > >> >> >> >> > <sushil.sush19us(a)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=… > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> >> On Mon, Jan 4, 2016 at 10:52 AM, < > >> >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> >> wrote: > >> >> >> >> >> Send yt-users mailing list submissions to > >> >> >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> >> >> > >> >> >> >> >> You can reach the person managing the list at > >> >> >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> >> >> To: Discussion of the yt analysis package > >> >> >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> >> >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> >> >> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > >> >> >> >> > > >> >> >> >> >> > >> >> >> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < > >> >> >> sushil.sush19us(a)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(a)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(a)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=… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > 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(a)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(a)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(a)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-v… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > >> >> >> >> > > >> >> >> >> >> > . > >> >> >> >> >> > > >> >> >> >> >> > 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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-request(a)lists.spacepope.org>> wrote: > >> >> >> >> >> > > >> >> >> >> >> > Send yt-users mailing list submissions to > >> >> >> >> >> > yt-users(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> >> >> > > >> >> >> >> >> > You can reach the person managing the list at > >> >> >> >> >> > yt-users-owner(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users-owner(a)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(a)gmail.com <mailto: > >> >> >> >> nathan12343(a)gmail.com>> > >> >> >> >> >> > To: Discussion of the yt analysis package > >> >> >> >> >> > <yt-users(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)lists.spacepope.org>> > >> >> >> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary > >> >> >> >> >> > volumes > >> >> >> >> >> > Message-ID: > >> >> >> >> >> > < > >> >> >> >> > >> >> >> >> > CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > >> >> >> >> <mailto: > >> >> >> >> > >> >> >> >> > >> >> >> >> > CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > >> >> >> >> > > >> >> >> >> >> > >>> > >> >> >> >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < > >> >> >> bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com > >> > >> >> >> wrote: > >> >> >> >> >> > >>>>> > >> >> >> >> >> > >>>>>> > >> >> >> >> >> > >>>>>> > >> >> >> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > >> >> >> >> bwoshea(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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/201… > >> >> >> >> < > >> >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> >> >> >> >> > >> >> >> >> >> > > >> >> >> >> >> > ------------------------------ > >> >> >> >> >> > > >> >> >> >> >> > Subject: Digest Footer > >> >> >> >> >> > > >> >> >> >> >> > _______________________________________________ > >> >> >> >> >> > yt-users mailing list > >> >> >> >> >> > yt-users(a)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(a)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(a)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/201… > >> >> >> >> > > >> >> >> >> >> > >> >> >> >> >> ------------------------------ > >> >> >> >> >> > >> >> >> >> >> Subject: Digest Footer > >> >> >> >> >> > >> >> >> >> >> _______________________________________________ > >> >> >> >> >> yt-users mailing list > >> >> >> >> >> yt-users(a)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(a)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/201… > >> >> >> >> > > >> >> >> >> > >> >> >> >> ------------------------------ > >> >> >> >> > >> >> >> >> Subject: Digest Footer > >> >> >> >> > >> >> >> >> _______________________________________________ > >> >> >> >> yt-users mailing list > >> >> >> >> yt-users(a)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(a)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/201… > >> >> >> > > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> Subject: Digest Footer > >> >> >> > >> >> >> _______________________________________________ > >> >> >> yt-users mailing list > >> >> >> yt-users(a)lists.spacepope.org > >> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> >> >> > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> End of yt-users Digest, Vol 95, Issue 11 > >> >> >> **************************************** > >> >> >> > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > *SK2* > >> >> > > >> >> > *"**Claiming that something can move faster than light is a good > >> >> > conversation-stopper in physics. People edge away from you in > >> >> > cocktail > >> >> > parties; friends never return phone calls. You just don?t mess with > >> >> > Albert > >> >> > Einstein.**"* > >> >> > > >> >> > > >> >> > _______________________________________________ > >> >> > yt-users mailing list > >> >> > yt-users(a)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/201… > > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users(a)lists.spacepope.org > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> >> > >> >> > >> >> ------------------------------ > >> >> > >> >> 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(a)lists.spacepope.org > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> 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(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > 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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

1 0

Error while using SlicePlot
by Sushilkumar Jan. 14, 2016

Jan. 14, 2016

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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 (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Jan 2016 14:01:37 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using SlicePlot > Message-ID: > <CALO3= > 5GMCcT_YiqYsp5jT6Ot252fqEeSgLAMdzB7CuPaw-nKZg(a)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(a)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(a)lists.spacepope.org> > > wrote: > >> > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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: Tue, 12 Jan 2016 10:03:41 -0600 > >> From: Nathan Goldbaum <nathan12343(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] Error while using SlicePlot > >> Message-ID: > >> > >> <CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g(a)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(a)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=sha… > >> > > >> > On Mon, Jan 11, 2016 at 4:27 PM, < > yt-users-request(a)lists.spacepope.org> > >> > wrote: > >> > > >> >> Send yt-users mailing list submissions to > >> >> yt-users(a)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(a)lists.spacepope.org > >> >> > >> >> You can reach the person managing the list at > >> >> yt-users-owner(a)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(a)gmail.com> > >> >> To: Discussion of the yt analysis package > >> >> <yt-users(a)lists.spacepope.org> > >> >> Subject: Re: [yt-users] Error while using SlicePlot > >> >> Message-ID: > >> >> <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= > >> >> LZdbzcHZg(a)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(a)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(a)lists.spacepope.org> > >> >> > wrote: > >> >> > > >> >> >> Send yt-users mailing list submissions to > >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> > >> >> >> You can reach the person managing the list at > >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> To: Discussion of the yt analysis package > >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> Subject: Re: [yt-users] Issue with loading data > >> >> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > >> >> >> jzuhone(a)gmail.com > >> >> >> http://www.jzuhone.com > >> >> >> > >> >> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar > >> >> >> > <sushil.sush19us(a)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=… > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> >> On Mon, Jan 4, 2016 at 10:52 AM, < > >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> wrote: > >> >> >> >> Send yt-users mailing list submissions to > >> >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> >> > >> >> >> >> You can reach the person managing the list at > >> >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> >> To: Discussion of the yt analysis package > >> >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> >> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > >> >> >> < > >> >> >> > >> >> > >> >> > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > >> >> >> > > >> >> >> >> > >> >> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < > >> >> sushil.sush19us(a)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(a)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(a)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=… > >> >> >> < > >> >> >> > >> >> > >> >> > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> < > >> >> >> > >> >> > >> >> > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > 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(a)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(a)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(a)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-v… > >> >> >> < > >> >> >> > >> >> > >> >> > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > >> >> >> > > >> >> >> >> > . > >> >> >> >> > > >> >> >> >> > 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(a)lists.spacepope.org <mailto: > >> >> >> yt-users-request(a)lists.spacepope.org>> wrote: > >> >> >> >> > > >> >> >> >> > Send yt-users mailing list submissions to > >> >> >> >> > yt-users(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> >> > > >> >> >> >> > You can reach the person managing the list at > >> >> >> >> > yt-users-owner(a)lists.spacepope.org <mailto: > >> >> >> yt-users-owner(a)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(a)gmail.com <mailto: > >> >> >> nathan12343(a)gmail.com>> > >> >> >> >> > To: Discussion of the yt analysis package > >> >> >> >> > <yt-users(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)lists.spacepope.org>> > >> >> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary > >> >> >> >> > volumes > >> >> >> >> > Message-ID: > >> >> >> >> > < > >> >> >> > CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > >> >> >> <mailto: > >> >> >> > >> >> >> > CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > >> >> >> < > >> >> >> > >> >> > >> >> > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > >> >> >> > > >> >> >> >> > >>> > >> >> >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < > >> >> bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com>> > >> >> wrote: > >> >> >> >> > >>>>> > >> >> >> >> > >>>>>> > >> >> >> >> > >>>>>> > >> >> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > >> >> >> bwoshea(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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/201… > >> >> >> < > >> >> >> > >> >> > >> >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> >> >> >> > >> >> >> >> > > >> >> >> >> > ------------------------------ > >> >> >> >> > > >> >> >> >> > Subject: Digest Footer > >> >> >> >> > > >> >> >> >> > _______________________________________________ > >> >> >> >> > yt-users mailing list > >> >> >> >> > yt-users(a)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(a)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(a)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/201… > >> >> >> > > >> >> >> >> > >> >> >> >> ------------------------------ > >> >> >> >> > >> >> >> >> Subject: Digest Footer > >> >> >> >> > >> >> >> >> _______________________________________________ > >> >> >> >> yt-users mailing list > >> >> >> >> yt-users(a)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(a)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/201… > >> >> >> > > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> Subject: Digest Footer > >> >> >> > >> >> >> _______________________________________________ > >> >> >> yt-users mailing list > >> >> >> yt-users(a)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(a)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/201… > >> >> > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users(a)lists.spacepope.org > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> >> > >> >> > >> >> ------------------------------ > >> >> > >> >> End of yt-users Digest, Vol 95, Issue 11 > >> >> **************************************** > >> >> > >> > > >> > > >> > > >> > -- > >> > *SK2* > >> > > >> > *"**Claiming that something can move faster than light is a good > >> > conversation-stopper in physics. People edge away from you in cocktail > >> > parties; friends never return phone calls. You just don?t mess with > >> > Albert > >> > Einstein.**"* > >> > > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)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/201… > > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> 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(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > 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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Error while using SlicePlot
by Sushilkumar Jan. 14, 2016

Jan. 14, 2016

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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: Tue, 12 Jan 2016 10:03:41 -0600 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using SlicePlot > Message-ID: > < > CAJXewOn9qs7TQ7EPaOee3H6wscm1U5acei-_+vBCQ3SaATQi7g(a)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(a)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=sha… > > > > On Mon, Jan 11, 2016 at 4:27 PM, <yt-users-request(a)lists.spacepope.org> > > wrote: > > > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] Error while using SlicePlot > >> Message-ID: > >> <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= > >> LZdbzcHZg(a)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(a)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(a)lists.spacepope.org> > >> > wrote: > >> > > >> >> Send yt-users mailing list submissions to > >> >> yt-users(a)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(a)lists.spacepope.org > >> >> > >> >> You can reach the person managing the list at > >> >> yt-users-owner(a)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(a)gmail.com> > >> >> To: Discussion of the yt analysis package > >> >> <yt-users(a)lists.spacepope.org> > >> >> Subject: Re: [yt-users] Issue with loading data > >> >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > >> >> jzuhone(a)gmail.com > >> >> http://www.jzuhone.com > >> >> > >> >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar < > sushil.sush19us(a)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=… > >> >> > > >> >> > > >> >> > > >> >> >> On Mon, Jan 4, 2016 at 10:52 AM, < > >> yt-users-request(a)lists.spacepope.org> > >> >> wrote: > >> >> >> Send yt-users mailing list submissions to > >> >> >> yt-users(a)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(a)lists.spacepope.org > >> >> >> > >> >> >> You can reach the person managing the list at > >> >> >> yt-users-owner(a)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(a)gmail.com> > >> >> >> To: Discussion of the yt analysis package > >> >> >> <yt-users(a)lists.spacepope.org> > >> >> >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > >> >> < > >> >> > >> > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > >> >> > > >> >> >> > >> >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < > >> sushil.sush19us(a)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(a)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(a)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=… > >> >> < > >> >> > >> > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > >> >> > > >> >> >> > > >> >> >> > > >> >> >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > >> >> < > >> >> > >> > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > >> >> > > >> >> >> > > >> >> >> > > >> >> >> > 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(a)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(a)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(a)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-v… > >> >> < > >> >> > >> > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > >> >> > > >> >> >> > . > >> >> >> > > >> >> >> > 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(a)lists.spacepope.org <mailto: > >> >> yt-users-request(a)lists.spacepope.org>> wrote: > >> >> >> > > >> >> >> > Send yt-users mailing list submissions to > >> >> >> > yt-users(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users-request(a)lists.spacepope.org> > >> >> >> > > >> >> >> > You can reach the person managing the list at > >> >> >> > yt-users-owner(a)lists.spacepope.org <mailto: > >> >> yt-users-owner(a)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(a)gmail.com <mailto: > >> >> nathan12343(a)gmail.com>> > >> >> >> > To: Discussion of the yt analysis package > >> >> >> > <yt-users(a)lists.spacepope.org <mailto: > >> >> yt-users(a)lists.spacepope.org>> > >> >> >> > Subject: Re: [yt-users] problem with slices in non-unitary > volumes > >> >> >> > Message-ID: > >> >> >> > < > >> >> CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > >> >> <mailto: > >> >> CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > >> >> < > >> >> > >> > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > >> >> > > >> >> >> > >>> > >> >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < > >> bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com>> > >> wrote: > >> >> >> > >>>>> > >> >> >> > >>>>>> > >> >> >> > >>>>>> > >> >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > >> >> bwoshea(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> yt-users(a)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/201… > >> >> < > >> >> > >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> >> >> > >> >> >> > > >> >> >> > ------------------------------ > >> >> >> > > >> >> >> > Subject: Digest Footer > >> >> >> > > >> >> >> > _______________________________________________ > >> >> >> > yt-users mailing list > >> >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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/201… > >> >> > > >> >> >> > >> >> >> ------------------------------ > >> >> >> > >> >> >> Subject: Digest Footer > >> >> >> > >> >> >> _______________________________________________ > >> >> >> yt-users mailing list > >> >> >> yt-users(a)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(a)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/201… > >> >> > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users(a)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(a)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/201… > >> > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > >> ------------------------------ > >> > >> End of yt-users Digest, Vol 95, Issue 11 > >> **************************************** > >> > > > > > > > > -- > > *SK2* > > > > *"**Claiming that something can move faster than light is a good > > conversation-stopper in physics. People edge away from you in cocktail > > parties; friends never return phone calls. You just don?t mess with > Albert > > Einstein.**"* > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > 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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

PlotCollection
by Junhwan Choi (최준환) Jan. 14, 2016

Jan. 14, 2016

Hi yt user, I have old yt script (with yt-2.7-ish) with eps_writer module that makes 3x3 multi panel slice plot as follow ================================= import matplotlib as matplotlib matplotlib.use('Agg') import matplotlib.pylab as pylab from yt.mods import * import yt.visualization.eps_writer as eps import pyx import pylab as pl pl.ion() pl.clf() # load up a dataset LBOX1 = 4000 LBOX2 = 4 LBOX3 = 0.04 index = 66 pf = load("../DD%04d/DD%04d" % (index,index)) den_center = pf.h.find_max("Density")[1] # create density slices pc = PlotCollection(pf, center=den_center) p1 =pc.add_slice("Density", "z", center=den_center, use_colorbar=False) p2 =pc.add_slice("Density", "x", center=den_center, use_colorbar=False) p3 =pc.add_slice("Density", "y", center=den_center, use_colorbar=False) p1.set_zlim(1e-27, 1e-20) p2.set_zlim(1e-27, 1e-20) p3.set_zlim(1e-27, 1e-20) p4 =pc.add_slice("Density", "z",center=den_center, use_colorbar=False) p5 =pc.add_slice("Density", "x",center=den_center, use_colorbar=False) p6 =pc.add_slice("Density", "y",center=den_center, use_colorbar=False) p4.set_zlim(2e-20, 2e-14) p5.set_zlim(2e-20, 2e-14) p6.set_zlim(2e-20, 2e-14) p7 =pc.add_slice("Density", "z",center=den_center, use_colorbar=False) p8 =pc.add_slice("Density", "x",center=den_center, use_colorbar=False) p9 =pc.add_slice("Density", "y",center=den_center, use_colorbar=False) p7.set_zlim(2e-16, 2e-10) p8.set_zlim(2e-16, 2e-10) p9.set_zlim(2e-16, 2e-10) p1.set_width(LBOX1,"pc") p2.set_width(LBOX1,"pc") p3.set_width(LBOX1,"pc") p4.set_width(LBOX2,"pc") p5.set_width(LBOX2,"pc") p6.set_width(LBOX2,"pc") p7.set_width(LBOX3,"pc") p8.set_width(LBOX3,"pc") p9.set_width(LBOX3,"pc") ep = eps.multiplot_yt(3,3,pc,bare_axes = True) ep.title_box("xy", loc=(0.1,2.95)) ep.title_box("yz", loc=(1.1,2.95)) ep.title_box("xz", loc=(2.1,2.95)) ep.scale_line(label="%6.0f kpc" % (LBOX1/4000.0), size=0.25, linewidth=pyx.style.linewidth.Thick, loc=(0.05,3.08)) ep.scale_line(label="%6.0f pc" % (LBOX2/4.0) , size=0.25, linewidth=pyx.style.linewidth.Thick, loc=(0.05,2.08)) ep.scale_line(label="%6.2f pc" % (LBOX3/4.0) , size=0.25, linewidth=pyx.style.linewidth.Thick, loc=(0.05,1.08)) ep.save_fig("VelDenSlice4R_%04d" % (index) ) pl.clf() ================================== And, now I would like to port to the latest yt. I could make most of changes but I found that there is no PlotCollection which can pass the figures to eps.multiplot_yt any more. Is there any alternative way to replace the what PlotCollection and add_slice did? I also need to include the annotate_xxx so that using imshow is not a good option for me. Thanks in advance, Junhwan Choi _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 5

Error while using SlicePlot
by Sushilkumar Jan. 12, 2016

Jan. 12, 2016

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=sha… On Mon, Jan 11, 2016 at 4:27 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using SlicePlot > Message-ID: > <CAJXewOkjMD3CCPbi6gseJK0Q2r2cHXews2EDm-cd= > LZdbzcHZg(a)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(a)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(a)lists.spacepope.org> > > wrote: > > > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] Issue with loading data > >> Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > >> jzuhone(a)gmail.com > >> http://www.jzuhone.com > >> > >> > On Jan 4, 2016, at 12:06 PM, Sushilkumar <sushil.sush19us(a)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=… > >> > > >> > > >> > > >> >> On Mon, Jan 4, 2016 at 10:52 AM, < > yt-users-request(a)lists.spacepope.org> > >> wrote: > >> >> Send yt-users mailing list submissions to > >> >> yt-users(a)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(a)lists.spacepope.org > >> >> > >> >> You can reach the person managing the list at > >> >> yt-users-owner(a)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(a)gmail.com> > >> >> To: Discussion of the yt analysis package > >> >> <yt-users(a)lists.spacepope.org> > >> >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > >> < > >> > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > >> > > >> >> > >> >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar < > sushil.sush19us(a)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(a)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(a)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=… > >> < > >> > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > >> > > >> >> > > >> >> > > >> >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > >> < > >> > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > >> > > >> >> > > >> >> > > >> >> > 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(a)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(a)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(a)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-v… > >> < > >> > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > >> > > >> >> > . > >> >> > > >> >> > 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(a)lists.spacepope.org <mailto: > >> yt-users-request(a)lists.spacepope.org>> wrote: > >> >> > > >> >> > Send yt-users mailing list submissions to > >> >> > yt-users(a)lists.spacepope.org <mailto: > >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> yt-users-request(a)lists.spacepope.org> > >> >> > > >> >> > You can reach the person managing the list at > >> >> > yt-users-owner(a)lists.spacepope.org <mailto: > >> yt-users-owner(a)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(a)gmail.com <mailto: > >> nathan12343(a)gmail.com>> > >> >> > To: Discussion of the yt analysis package > >> >> > <yt-users(a)lists.spacepope.org <mailto: > >> yt-users(a)lists.spacepope.org>> > >> >> > Subject: Re: [yt-users] problem with slices in non-unitary volumes > >> >> > Message-ID: > >> >> > < > >> CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > >> <mailto: > >> CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > >> < > >> > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > >> > > >> >> > >>> > >> >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea < > bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com>> wrote: > >> >> > >>>>> > >> >> > >>>>>> > >> >> > >>>>>> > >> >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > >> bwoshea(a)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(a)lists.spacepope.org <mailto: > >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> yt-users(a)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(a)lists.spacepope.org <mailto: > >> yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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/201… > >> < > >> > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> >> > >> >> > > >> >> > ------------------------------ > >> >> > > >> >> > Subject: Digest Footer > >> >> > > >> >> > _______________________________________________ > >> >> > yt-users mailing list > >> >> > yt-users(a)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(a)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(a)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/201… > >> > > >> >> > >> >> ------------------------------ > >> >> > >> >> Subject: Digest Footer > >> >> > >> >> _______________________________________________ > >> >> yt-users mailing list > >> >> yt-users(a)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(a)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/201… > >> > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)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(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 95, Issue 11 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"* _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

yt_data - Invitation to collaborate
by Sushilkumar Sreekumar (via Google Drive) Jan. 11, 2016

Jan. 11, 2016

I've shared an item with you: yt_data https://drive.google.com/folderview?id=0B4g8shg4DL7oak5PLWVVdG5UMHc&usp=sha… It's not an attachment – it's stored online. To open this item, just click the link above. Dear yt: Python script and the file from which the data is read and formatted as numpy arrays and SlicePlot is used _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

1 0

Error while using SlicePlot
by Sushilkumar Jan. 11, 2016

Jan. 11, 2016

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Issue with loading data > Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > jzuhone(a)gmail.com > http://www.jzuhone.com > > > On Jan 4, 2016, at 12:06 PM, Sushilkumar <sushil.sush19us(a)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=… > > > > > > > >> On Mon, Jan 4, 2016 at 10:52 AM, <yt-users-request(a)lists.spacepope.org> > wrote: > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > < > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > > > >> > >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar <sushil.sush19us(a)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(a)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(a)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=… > < > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > > > >> > > >> > > >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > < > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > > > >> > > >> > > >> > 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(a)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(a)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(a)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-v… > < > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > > > >> > . > >> > > >> > 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(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> wrote: > >> > > >> > Send yt-users mailing list submissions to > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> > >> > > >> > You can reach the person managing the list at > >> > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)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(a)gmail.com <mailto: > nathan12343(a)gmail.com>> > >> > To: Discussion of the yt analysis package > >> > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org>> > >> > Subject: Re: [yt-users] problem with slices in non-unitary volumes > >> > Message-ID: > >> > < > CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > <mailto: > CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > < > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > > > >> > >>> > >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com>> wrote: > >> > >>>>> > >> > >>>>>> > >> > >>>>>> > >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > bwoshea(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)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(a)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/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > >> > > >> > ------------------------------ > >> > > >> > Subject: Digest Footer > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)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(a)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(a)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/201… > > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)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(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 1

yt install_script vs Blue Waters SSL
by Levy, Stuart A Jan. 10, 2016

Jan. 10, 2016

Hello yt people, I'm trying to install current yt-3.3dev on Blue Waters at NCSA, using the install_script.sh route. After hacking around the fact that it has an obsolete & unsafe openssl library as the default (I needed to pass LDFLAGS/CPPFLAGS to the python build to set the -L and -rpath to the non-default usable openssl), I'm having lots of trouble getting other component installs to work. The yt_install.log has things like Processing dependencies for matplotlib==1.4.3 Searching for pytz Reading https://pypi.python.org/simple/pytz/ Download error on https://pypi.python.org/simple/pytz/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581) -- Some packages may not be found! Couldn't find index page for 'pytz' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.python.org/simple/ Download error on https://pypi.python.org/simple/: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:581) -- Some packages may not be found! No local packages or download links found for pytz error: Could not find suitable distribution for Requirement.parse('pytz') Yet when I run what seems like the same install by hand ($DIR/bin/pip -v install pytz) it works fine, without error. I can then re-run install_script.sh, until it reaches the next dependency and fails, etc. Each cycle takes 5-10 minutes so it's pretty tedious. ***=> I don't understand why the internal-to-matplotlib-setup call to pip fails, while it succeeds when I run it by hand. A suspicion: could the CERTIFICATE_VERIFY_FAILED errors be hinting that Blue Waters has an https gateway to the outside world that rewrites SSL certificates? I don't know whether that's true. This page suggested a way to grab the needed root certificate and point env var PIP_CERT at it... http://stackoverflow.com/questions/25981703/pip-install-fails-with-connecti… but trying that didn't help in this case. The yt-installed "pip" works fine when run by hand, but whatever matplotlib's setup.py is running still fails. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 2

Issue with loadtxt
by Sushilkumar Jan. 7, 2016

Jan. 7, 2016

Dear yt: I am currently having issues with yt.loadtxt. It gives me the following error. I am the getting the following error File "numpy_loadtxt.py", line 3, in <module> b = yt.loadtxt("u25.dat") AttributeError: 'module' object has no attribute 'loadtxt' I am currently using version 3.2.2 yt module located at: /state/partition1/anaconda/lib/python2.7/site-packages The current version and changeset for the code is: --- Version = 3.2.2 Changeset = None --- I am using the example for loadtxt as mentioned here http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… Thanks in advance On Mon, Jan 4, 2016 at 11:10 AM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Issue with loading data > Message-ID: <BF0E1EAF-D72D-483C-98FC-3C08C9968667(a)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(a)cfa.harvard.edu > jzuhone(a)gmail.com > http://www.jzuhone.com > > > On Jan 4, 2016, at 12:06 PM, Sushilkumar <sushil.sush19us(a)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=… > > > > > > > >> On Mon, Jan 4, 2016 at 10:52 AM, <yt-users-request(a)lists.spacepope.org> > wrote: > >> Send yt-users mailing list submissions to > >> yt-users(a)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(a)lists.spacepope.org > >> > >> You can reach the person managing the list at > >> yt-users-owner(a)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(a)gmail.com> > >> To: Discussion of the yt analysis package > >> <yt-users(a)lists.spacepope.org> > >> Subject: Re: [yt-users] problem with yt update to 3.0 > >> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022(a)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-a… > < > http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-a… > > > >> > >> > On Dec 30, 2015, at 12:01 PM, Sushilkumar <sushil.sush19us(a)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(a)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(a)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=… > < > http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… > > > >> > > >> > > >> > 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(a)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(a)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/d9502d84802972ba3e644d2d5c47b87f73… > < > https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73… > > > >> > > >> > > >> > 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(a)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(a)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(a)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-v… > < > http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-v… > > > >> > . > >> > > >> > 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(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> wrote: > >> > > >> > Send yt-users mailing list submissions to > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> > >> > > >> > You can reach the person managing the list at > >> > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)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(a)gmail.com <mailto: > nathan12343(a)gmail.com>> > >> > To: Discussion of the yt analysis package > >> > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org>> > >> > Subject: Re: [yt-users] problem with slices in non-unitary volumes > >> > Message-ID: > >> > < > CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)mail.gmail.com > <mailto: > CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g(a)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(a)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(a)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(a)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-creati… > < > https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creati… > > > >> > >>> > >> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea(a)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(a)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(a)gmail.com <mailto:nathan12343@gmail.com>> wrote: > >> > >>>>> > >> > >>>>>> > >> > >>>>>> > >> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea < > bwoshea(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users(a)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(a)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(a)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/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > >> > > >> > ------------------------------ > >> > > >> > Subject: Digest Footer > >> > > >> > _______________________________________________ > >> > yt-users mailing list > >> > yt-users(a)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(a)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(a)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/201… > > > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)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(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)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(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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