[yt-users] problem with yt update to 3.0
Nathan Goldbaum
nathan12343 at gmail.com
Sat Dec 26 09:43:46 PST 2015
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:
>>>
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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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>>>> >>>>>
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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
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>
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>
> *"**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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