[yt-users] problem with yt update to 3.0

Nathan Goldbaum nathan12343 at gmail.com
Sat Dec 26 08:41:09 PST 2015


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:
>
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>> 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
>> >>>>>>>
>> >>>>>>>
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>> >>>>>>>
>> >>>>>>
>> >>>>>
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