[yt-users] problem with yt update to 3.0
Sushilkumar
sushil.sush19us at gmail.com
Sat Dec 26 08:39:45 PST 2015
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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> 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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