[yt-users] problem with yt update to 3.0
Sushilkumar
sushil.sush19us at gmail.com
Sat Dec 26 10:30:44 PST 2015
Dear Nathan:
I will try it and let you know. In the meanwhile, could you let me know if
yt supports loading text file for version 2.6.1? If so could you point me
to examples for the same.
Thanks in advance
On Sat, Dec 26, 2015, 11:44 Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> 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
>>>>> >>>>>>>
>>>>> >>>>>>>
>>>>> >>>>>>> _______________________________________________
>>>>> >>>>>>> yt-users mailing list
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>>>>> >>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>> >>>>>>>
>>>>> >>>>>>>
>>>>> >>>>>>
>>>>> >>>>>
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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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>>>> yt-users at lists.spacepope.org
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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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