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-ve... . 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@lists.spacepope.org> wrote:
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Today's Topics:
1. Re: problem with slices in non-unitary volumes (Nathan Goldbaum)
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Message: 1 Date: Wed, 23 Dec 2015 17:17:56 -0600 From: Nathan Goldbaum <nathan12343@gmail.com> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org> Subject: Re: [yt-users] problem with slices in non-unitary volumes Message-ID: < CAJXewOmVEX-qB41doTk+7DT1AOLsn53KMb8nvfr8dwyFrKY-4g@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@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@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@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-creatin...
On Wed, Dec 23, 2015 at 4:08 PM, Brian O'Shea <bwoshea@gmail.com>
wrote:
Oh, interesting. Is there a way to circumvent auto-detection of
On Wed, Dec 23, 2015 at 4:35 PM, Nathan Goldbaum <
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@gmail.com> wrote:
> > > On Wed, Dec 23, 2015 at 11:20 AM, Brian O'Shea <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
fields? 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@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >
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