[yt-users] Issue with loading data
Sushilkumar
sushil.sush19us at gmail.com
Mon Jan 4 09:06:41 PST 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=load_uniform_grid
On Mon, Jan 4, 2016 at 10:52 AM, <yt-users-request at lists.spacepope.org>
wrote:
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> Today's Topics:
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> 1. Re: problem with yt update to 3.0 (John ZuHone)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Jan 2016 11:52:03 -0500
> From: John ZuHone <jzuhone at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] problem with yt update to 3.0
> Message-ID: <E58E10EE-846A-4595-87EC-47CAF9CDA022 at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> In the current development version of yt there is also yt.loadtxt, which
> is essentially a wrapper for numpy.loadtxt which also accepts unit
> information.
>
> See
> http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk
> <
> http://yt-project.org/docs/dev/analyzing/units/symbolic_units.html#Saving-and-Loading-YTArrays-to/from-disk
> >
>
> > On Dec 30, 2015, at 12:01 PM, Sushilkumar <sushil.sush19us at gmail.com>
> wrote:
> >
> > Dear Nathan:
> >
> > As per your advice I am trying to load my text file to numpy array. But
> there are two ways to so using numpy.loadtxt and numpy.fromfile. Could you
> suggest which of them is more efficient for large files and more suitable
> for yt (if any)?
> >
> > Thanks in advance
> >
> > On Sat, Dec 26, 2015 at 6:43 PM, Sushilkumar Sreekumar <
> sushil.sush19us at gmail.com <mailto:sushil.sush19us at gmail.com>> wrote:
> > Dear Nathan:
> >
> >
> >
> > Thank you for your help
> >
> >
> >
> > --
> > SK2
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
> >
> >
> >
> > From: Nathan Goldbaum <mailto:nathan12343 at gmail.com>
> > Sent: Saturday, December 26, 2015 12:34 PM
> > To: Sushilkumar <mailto:sushil.sush19us at gmail.com>
> > Cc: Discussion of the yt analysis package <mailto:
> yt-users at lists.spacepope.org>
> > Subject: Re: [yt-users] problem with yt update to 3.0
> >
> >
> >
> > If you can format your data as numpy arrays, there are examples of how
> to load your data into yt here:
> >
> >
> >
> >
> http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
> <
> http://yt-project.org/docs/2.6/examining/generic_array_data.html?highlight=load_uniform_grid
> >
> >
> >
> > yt (2.6.1 or newer) does not support i/o from arbitrary text files.
> >
> >
> >
> > On Sat, Dec 26, 2015 at 12:30 PM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto:sushil.sush19us at gmail.com>> wrote:
> >
> > Dear Nathan:
> >
> > I will try it and let you know. In the meanwhile, could you let me know
> if yt supports loading text file for version 2.6.1? If so could you point
> me to examples for the same.
> >
> > Thanks in advance
> >
> >
> >
> > On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <nathan12343 at gmail.com
> <mailto:nathan12343 at gmail.com>> wrote:
> >
> > This is happening because python is unable to link against an openSSL
> library.
> >
> >
> >
> > Can you try using the get_yt.sh script install of the install_script.sh
> script:
> >
> >
> >
> >
> https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh
> <
> https://bitbucket.org/yt_analysis/yt/raw/d9502d84802972ba3e644d2d5c47b87f73a6bd08/doc/get_yt.sh
> >
> >
> >
> > This script installs yt using the miniconda python distribution, which
> includes a precompiled python and openSSL library.
> >
> >
> >
> > -Nathan
> >
> >
> >
> > On Sat, Dec 26, 2015 at 11:40 AM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto:sushil.sush19us at gmail.com>> wrote:
> >
> > Hi Nathan:
> >
> > Thanks for your reply.
> >
> > I had done that before installing version 2.X. I used to get errors as
> below. Even now I keep getting the same error after reinstalling from
> scratch. The error comes after "installing pip". I tried it on my pc and
> also on cluster but same issues.
> >
> > ********************************************
> > FAILURE REPORT:
> > ********************************************
> >
> > bootstrap(tmpdir=tmpdir)
> > File "get-pip.py", line 82, in bootstrap
> > import pip
> > File "/tmp/tmpxKqAjR/pip.zip/pip/__init__.py", line 15, in <module>
> > File "/tmp/tmpxKqAjR/pip.zip/pip/vcs/subversion.py", line 9, in
> <module>
> > File "/tmp/tmpxKqAjR/pip.zip/pip/index.py", line 30, in <module>
> > File "/tmp/tmpxKqAjR/pip.zip/pip/wheel.py", line 35, in <module>
> > File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/scripts.py", line 14,
> in <module>
> > File "/tmp/tmpxKqAjR/pip.zip/pip/_vendor/distlib/compat.py", line 31,
> in <module>
> > ImportError: cannot import name HTTPSHandler
> >
> > ********************************************
> > ********************************************
> > Failure. Check /home/adrith/yt-x86_64/yt_install.log. The last 10
> lines are above.
> >
> >
> >
> > On Sat, Dec 26, 2015 at 10:41 AM, Nathan Goldbaum <nathan12343 at gmail.com
> <mailto:nathan12343 at gmail.com>> wrote:
> >
> > Hi Sushilkumar,
> >
> >
> >
> > Can you try reinstalling yt from scratch?
> >
> >
> >
> > -Nathan
> >
> >
> >
> > On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto:sushil.sush19us at gmail.com>> wrote:
> >
> > Dear yt:
> >
> > I am currently running yt version 2.6.1 and want to update to version 3
> (to read text files). Could you provide me link to so?
> >
> > I tried it using yt update --all as per the link
> >
> >
> http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back
> <
> http://yt-project.org/doc/yt3differences.html#updating-to-yt-3-0-from-old-versions-and-going-back
> >
> > .
> >
> > But it wont update to 3.0 and still shows as 2.6.1
> >
> > Kindly help
> >
> > Thanks in advance
> >
> > sushilkumar
> >
> >
> >
> > On Thu, Dec 24, 2015 at 12:25 PM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
> >
> > Send yt-users mailing list submissions to
> > yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > or, via email, send a message with subject or body 'help' to
> > yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>
> >
> > You can reach the person managing the list at
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of yt-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 23 Dec 2015 17:17:56 -0600
> > From: Nathan Goldbaum <nathan12343 at gmail.com <mailto:
> nathan12343 at gmail.com>>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > Subject: Re: [yt-users] problem with slices in non-unitary volumes
> > Message-ID:
> > <
> CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g at mail.gmail.com
> <mailto:
> CAJXewOmVEX-qB41doTk%2B7DT1AOLsn53KMb8nvfr8dwyFrKY-4g at mail.gmail.com>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > I get the same error over here. I think it's unrelated to the other
> error.
> > The relevant portion of the C stack trace is here:
> >
> > Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
> > 0 libsystem_kernel.dylib 0x00007fff8b615286 __pthread_kill + 10
> > 1 libsystem_c.dylib 0x00007fff8bc2a9ab abort + 129
> > 2 libsystem_malloc.dylib 0x00007fff915d5fe2 szone_error + 625
> > 3 libsystem_malloc.dylib 0x00007fff915cf374
> > small_free_list_remove_ptr + 154
> > 4 libsystem_malloc.dylib 0x00007fff915cac3f
> > szone_free_definite_size + 1856
> > 5 multiarray.so 0x00000001044c2d16 npy_free_cache + 70
> > 6 multiarray.so 0x00000001044c6ed6 array_dealloc + 182
> > 7 selection_routines.so 0x00000001063ffe34
> > __pyx_pw_2yt_8geometry_18selection_routines_13SliceSelector_3fill_mask +
> > 8804 (selection_routines.c:19749)
> >
> > Line 19749 of selection_routines.c corresponds to line 1158 in
> > selection_routines.pyx, which is the place where the fill_mask member
> > variable of the SliceSelector extension type gets defined.
> >
> > Unfortunately, I have no idea how to debug this from here...
> >
> > -Nathan
> >
> > On Wed, Dec 23, 2015 at 4:57 PM, Brian O'Shea <bwoshea at gmail.com
> <mailto:bwoshea at gmail.com>> wrote:
> >
> > > Actually, interesting followup here - I have to take it back. When I
> do a
> > > projection plot:
> > >
> > > yt.ProjectionPlot(ds,'x',("gas",
> > > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
> > >
> > > the behavior is perfectly fine and I get projections that look
> sensible.
> > > *however*, when I do a slice plot:
> > >
> > > yt.SlicePlot(ds,'x',("gas",
> > > "temperature"),center=[0.0,0.0,0.0],width=(0.2,'Mpc')).save()
> > >
> > > I get a malloc error:
> > >
> > > yt : [INFO ] 2015-12-23 17:50:59,082 Gathering a field list (this
> may
> > > take a moment.)
> > > yt : [INFO ] 2015-12-23 17:50:59,155 Loading field plugins.
> > > yt : [INFO ] 2015-12-23 17:50:59,155 Loaded angular_momentum (8 new
> > > fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded astro (16 new fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded cosmology (23 new
> fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,156 Loaded fluid (64 new fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded fluid_vector (96 new
> > > fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded geometric (112 new
> fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded local (112 new fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,157 Loaded magnetic_field (120 new
> > > fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,158 Loaded my_plugins (120 new
> fields)
> > > yt : [INFO ] 2015-12-23 17:50:59,158 Loaded species (122 new
> fields)
> > > python2.7(12254,0x7fff72d19310) malloc: *** error for object
> 0x103e39008:
> > > incorrect checksum for freed object - object was probably modified
> after
> > > being freed.
> > > *** set a breakpoint in malloc_error_break to debug
> > > Abort trap: 6
> > >
> > > This happens on my Mac (OS X 10.9.5, LLVM v6.0) and also on my Linux
> > > machine (Ubuntu 13.04, gcc 4.6.3), although on the linux machine I
> just get
> > > a seg fault instead of the malloc stuff. Using pdb (python -m pdb
> > > crashing_script.py) gives me the same error with no additional
> information.
> > >
> > >
> > > On Wed, Dec 23, 2015 at 5:40 PM, Brian O'Shea <bwoshea at gmail.com
> <mailto:bwoshea at gmail.com>> wrote:
> > >
> > >> Bugfix confirmed; this works for me as well. Thank you very much!
> > >>
> > >> On Wed, Dec 23, 2015 at 5:18 PM, Nathan Goldbaum <
> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>>
> > >> wrote:
> > >>
> > >>> I've opened a pull request that allows me to load your dataset:
> > >>>
> > >>>
> > >>>
> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
> <
> https://bitbucket.org/yt_analysis/yt/pull-requests/1915/bugfix-avoid-creating-particle-unions-for/diff
> >
> > >>>
> > >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea at gmail.com
> <mailto:bwoshea at gmail.com>> wrote:
> > >>>
> > >>>> Oh, interesting. Is there a way to circumvent auto-detection of
> fields?
> > >>>>
> > >>>> On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>
> > >>>> > wrote:
> > >>>>
> > >>>>> It looks like field detection is breaking for this Enzo-3.0 active
> > >>>>> particle dataset. StoredEnergy is available on-disk as
> ('AGNParticle,
> > >>>>> 'StoredEnergy'), but for some reason the field detection system
> isn't able
> > >>>>> to guess that.
> > >>>>>
> > >>>>> On Wed, Dec 23, 2015 at 3:19 PM, Nathan Goldbaum <
> > >>>>> nathan12343 at gmail.com <mailto:nathan12343 at gmail.com>> wrote:
> > >>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <bwoshea at gmail.com
> <mailto:bwoshea at gmail.com>>
> > >>>>>> wrote:
> > >>>>>>
> > >>>>>>> Dear yt-users,
> > >>>>>>>
> > >>>>>>> I'm having a problem with making slices in non-unitary volumes.
> I
> > >>>>>>> have a 3D enzo simulation that has domain bounds of (-1.6...1.6)
> in every
> > >>>>>>> dimension (units of megaparsecs), and after I updated to the tip
> of yt-3
> > >>>>>>> (changeset d9502d848029) from a fairly old version of the code I
> suddenly
> > >>>>>>> have problems with making simple projections. If I run this set
> of
> > >>>>>>> commands:
> > >>>>>>>
> > >>>>>>>
> > >>>>>> Any idea which version you updated from? I tried on yt-3.1 and get
> > >>>>>> the same error. This is just so we can bisect and find the change
> that
> > >>>>>> introduced the regression.
> > >>>>>>
> > >>>>>>
> > >>>>>>> import yt
> > >>>>>>> ds = yt.load("DD0400/DD0400")
> > >>>>>>> proj =
> > >>>>>>>
> yt.SlicePlot(ds,'x','temperature',center=[0.0,0.0,0.0],width=(0.2,'Mpc'))
> > >>>>>>>
> > >>>>>>> I get this error:
> > >>>>>>>
> > >>>>>>> http://paste.yt-project.org/show/6115/ <
> http://paste.yt-project.org/show/6115/>
> > >>>>>>>
> > >>>>>>> This seems to work fine on an Enzo cosmological dataset (domain
> > >>>>>>> bounds 0-1 in each dimension), and previously worked fine in
> yt-3 (using a
> > >>>>>>> version of the code from a couple of months ago).
> > >>>>>>>
> > >>>>>>> is this a bug, or am I doing something dumb?
> > >>>>>>>
> > >>>>>>> Thanks!
> > >>>>>>>
> > >>>>>>> --Brian
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> _______________________________________________
> > >>>>>>> yt-users mailing list
> > >>>>>>> yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>
> > >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> yt-users mailing list
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> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > >>>>>
> > >>>>>
> > >>>>
> > >>>> _______________________________________________
> > >>>> yt-users mailing list
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> > >>>>
> > >>>>
> > >>>
> > >>> _______________________________________________
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> > >>>
> > >>
> > >
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> >
> >
> >
> > --
> >
> > SK2
> >
> >
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> >
> >
> >
> >
> >
> > --
> >
> > SK2
> >
> >
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > SK2
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
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--
*SK2*
*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*
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