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/d9502d84802972ba3e644d2d5c47b87f73a...
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
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
wrote: Hi Sushilkumar,
Can you try reinstalling yt from scratch?
-Nathan
On Sat, Dec 26, 2015 at 10:39 AM, Sushilkumar
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-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,
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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
To: Discussion of the yt analysis package 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
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
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
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@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 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 >>>>> >>>>> >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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