[yt-users] problem with yt update to 3.0

Nathan Goldbaum nathan12343 at gmail.com
Sat Dec 26 10:33:45 PST 2015


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

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>
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> 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
>>
>> 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>
>> 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
>>> > 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> 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
>>>>> .
>>>>>
>>>>> 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> wrote:
>>>>>
>>>>>> Send yt-users mailing list submissions to
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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>
>>>>>> To: Discussion of the yt analysis package
>>>>>>         <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>
>>>>>> 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>
>>>>>> 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>
>>>>>> 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>
>>>>>> >> 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
>>>>>> >>>
>>>>>> >>> On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <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
>>>>>> >>>> > 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> wrote:
>>>>>> >>>>>
>>>>>> >>>>>>
>>>>>> >>>>>>
>>>>>> >>>>>> On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <
>>>>>> 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/
>>>>>> >>>>>>>
>>>>>> >>>>>>> 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
>>>>>> >>>>>>>
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>>> >>>>>>>
>>>>>> >>>>>>>
>>>>>> >>>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> yt-users mailing list
>>>>>> >>>>> yt-users at lists.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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>>>>>> >>>
>>>>>> >>>
>>>>>> >>
>>>>>> >
>>>>>> > _______________________________________________
>>>>>> > yt-users mailing list
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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
>>>>> 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.**"*
>>>
>>>
>>
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