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January 2016

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Issue with loading data
by Sushilkumar Jan. 4, 2016

Jan. 4, 2016

Dear yt: I am currently using version 2.6.1 and will be updating to 3.x soon. But in the meanwhile is there a way to load data using numpy array. Using link http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=… My script and the corresponding error is below. from yt.mods import * import numpy as np from yt.utilities.physical_constants import cm_per_kpc, cm_per_mpc ms = 1536 vector_max=ms-(ms/3) vector = np.genfromtxt("u25.mtx",skip_header=2,skip_footer=vector_max,usecols=1) data =dict(Density=vector) bbox = np.array([[-4, 3], [-4, 3], [-4, 3]]) pf = load_uniform_grid(data, vector.shape, cm_per_mpc, bbox=bbox, nprocs=3) ERROR: Traceback (most recent call last): File "numpy_loadtxt.py", line 14, in <module> pf = load_uniform_grid(data, vector.shape, cm_per_mpc, bbox=bbox, nprocs=64) File "/home/sushilkumar.sreekuma/yt/yt-x86_64/src/yt-hg/yt/frontends/stream/data_structures.py", line 475, in load_uniform_grid decompose_array(data[key], psize, bbox) File "/home/sushilkumar.sreekuma/yt/yt-x86_64/src/yt-hg/yt/utilities/decompose.py", line 44, in decompose_array bbox[2, 0]:bbox[2, 1]:d_s[2]] File "/home/sushilkumar.sreekuma/yt/yt-x86_64/lib/python2.7/site-packages/numpy/lib/index_tricks.py", line 166, in __getitem__ nn = _nx.indices(size, typ) File "/home/sushilkumar.sreekuma/yt/yt-x86_64/lib/python2.7/site-packages/numpy/core/numeric.py", line 1602, in indices res = empty((N,)+dimensions, dtype=dtype) ValueError: negative dimensions are not allowed Thank you 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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Issue with loading data
by Sushilkumar Jan. 4, 2016

Jan. 4, 2016

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@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@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> > > >>> > > >>> > > >> > > > > > > _______________________________________________ > > > 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

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Re: [yt-users] problem with yt update to 3.0
by Sushilkumar Jan. 4, 2016

Jan. 4, 2016

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… . 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> 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 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> > To: Discussion of the yt analysis package > <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> > 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> 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> 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 > > > >> 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… > >>> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea(a)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 > >>>> > 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> wrote: > >>>>> > >>>>>> > >>>>>> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <bwoshea(a)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/ > >>>>>>> > >>>>>>> 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 > >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>>>>>> > >>>>>>> > >>>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> yt-users mailing list > >>>>> yt-users(a)lists.spacepope.org > >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>>>> > >>>>> > >>>> > >>>> _______________________________________________ > >>>> yt-users mailing list > >>>> yt-users(a)lists.spacepope.org > >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>>> > >>>> > >>> > >>> _______________________________________________ > >>> yt-users mailing list > >>> yt-users(a)lists.spacepope.org > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >>> > >>> > >> > > > > _______________________________________________ > > 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 94, Issue 24 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. 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