[yt-users] problem with yt update to 3.0
Sushilkumar
sushil.sush19us at gmail.com
Sat Dec 26 09:40:21 PST 2015
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:
>>
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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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>>
>>
>>
>> --
>> *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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>
--
*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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