[yt-users] amr_utils

Agarwal, Shankar sagarwal at ku.edu
Sat Feb 6 12:01:34 PST 2010


Matt,

Something going wrong with numpy.



[agarwa23 at tg-steele RD0001]$ python hop_yt.py 
yt.lagos   INFO       2010-02-06 14:54:40,898 No HDF4 support
yt.lagos   WARNING    2010-02-06 14:54:40,981 No h5py. Data serialization disabled.
Traceback (most recent call last):
  File "hop_yt.py", line 7, in <module>
    from yt.mods import *
  File "/autohome/u118/agarwa23/enzov1.5/src/yt/yt/mods.py", line 32, in <module>
    import yt.lagos as lagos
  File "/autohome/u118/agarwa23/enzov1.5/src/yt/yt/lagos/__init__.py", line 47, in <module>
    from yt.arraytypes import *
  File "/autohome/u118/agarwa23/enzov1.5/src/yt/yt/arraytypes.py", line 30, in <module>
    import numpy as na
  File "/home/ba01/u118/agarwa23/enzov1.5/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/__init__.py", line 130, in <module>
    import add_newdocs
  File "/home/ba01/u118/agarwa23/enzov1.5/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/add_newdocs.py", line 9, in <module>
    from lib import add_newdoc
  File "/home/ba01/u118/agarwa23/enzov1.5/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/lib/__init__.py", line 13, in <module>
    from polynomial import *
  File "/home/ba01/u118/agarwa23/enzov1.5/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/lib/polynomial.py", line 11, in <module>
    import numpy.core.numeric as NX
AttributeError: 'module' object has no attribute 'core'



-----Original Message-----
From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
Sent: Sat 2/6/2010 1:36 PM
To: Discussion of the yt analysis package
Subject: Re: [yt-users] amr_utils
 
Hi Shankar,

Glad it succeeded! Don't worry about finishing up with hg. It's still  
optional. You should now just be able to use yt as before. :)

Good luck,

Matt



On Feb 6, 2010, at 11:28 AM, "Agarwal, Shankar" <sagarwal at ku.edu> wrote:

> Hi Matt,
>
>
> My modules are
>
>  1) java/1.6.0_14   2) mpfr/2.4.1      3) gcc/4.4.0
>
>
>
> My yt build failed due to Mercurial...
>
> Downloading http://mercurial.selenic.com/release/ 
> mercurial-1.4.3.tar.gz
> Processing mercurial-1.4.3.tar.gz
> Running mercurial-1.4.3/setup.py -q bdist_egg --dist-dir /tmp/ 
> easy_install-lXCfn0/mercurial-1.4.3/egg-dist-tmp-SHK1v5
> Traceback (most recent call last):
>  File "/home/ba01/u118/agarwa23/enzo1.5/src/yt/doc/yt-x86_64/bin/ 
> easy_install-2.6", line 8, in <module>
>    load_entry_point('setuptools==0.6c9', 'console_scripts',  
> 'easy_install-2.6')()
>
>
>
>
> Should I set INST_HG = 0 ?
>
> INST_WXPYTHON   = 1 so I will  be installing wxPython
> INST_ZLIB       = 1 so I will  be installing zlib
> INST_HG         = 1 so I will  be installing Mercurial
> INST_TRAITS     = 0 so I won't be installing Traits
>
>
> Shankar
>
>
>
>
> -----Original Message-----
> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
> Sent: Sat 2/6/2010 12:02 PM
> To: Discussion of the yt analysis package
> Subject: Re: [yt-users] amr_utils
>
> Hi Shankar,
>
> This thread is from when you installed yt on Steele several months  
> ago.
>
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2009-November/000234.html
>
> Looks like back then you had to swap out intel for GNU back then, too.
> If you do that now, and wipe/rebuild as I sent you, it should work
> out okay.
>
> Best,
>
> Matt
>
> On Sat, Feb 6, 2010 at 9:56 AM, Matthew Turk <matthewturk at gmail.com>  
> wrote:
>> No, this looks more like there are issues with your compiler, and
>> components of yt being compiled with Intel. Â Compiling yt with
>> anything other than GNU is tricky.
>>
>> You can try flushing it out with this:
>>
>> find /autohome/u118/agarwa23/enzo1.5/src/yt/ -name "*.so" |xargs rm  
>> -v
>> find /autohome/u118/agarwa23/enzo1.5/src/yt/ -name "*.o" |xargs rm -v
>>
>> and then re-build. Â Make sure that if you are on a machine with
>> modules you have the GNU modules loaded, not the Intel modules before
>> this.
>>
>> -Matt
>>
>> On Sat, Feb 6, 2010 at 9:51 AM, Agarwal, Shankar <sagarwal at ku.edu>  
>> wrote:
>>> Ok. But now I get this...
>>>
>>> Traceback (most recent call last):
>>> Â File "visual.py", line 6, in <module>
>>> Â  Â from yt.mods import *
>>> Â File "/autohome/u118/agarwa23/enzo1.5/src/yt/yt/mods.py", line 
>>>  32, in <module>
>>> Â  Â import yt.lagos as lagos
>>> Â File "/autohome/u118/agarwa23/enzo1.5/src/yt/yt/lagos/__init__ 
>>> .py", line 66, in <module>
>>> Â  Â import PointCombine
>>> ImportError: /autohome/u118/agarwa23/enzo1.5/src/yt/yt/lagos/ 
>>> PointCombine.so: undefined symbol: _intel_fast_memset
>>>
>>>
>>> Do you think my older version is somehow clashing with the new one?
>>>
>>> Shankar
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: yt-users-bounces at lists.spacepope.org on behalf of Matthew Turk
>>> Sent: Sat 2/6/2010 11:46 AM
>>> To: Discussion of the yt analysis package
>>> Subject: Re: [yt-users] amr_utils
>>>
>>> Hi Shankar,
>>>
>>> Looks like you're inside an enzo svn checkout. Â To update your  
>>> entire
>>> enzo+yt source tree (which, because yt is included via  
>>> svn:externals)
>>> you should do:
>>>
>>> /autohome/u118/agarwa23/enzo1.5/
>>> svn up
>>> cd src/yt
>>> python2.6 setup.py build_ext -i
>>>
>>> This will (in order) put you in the root enzo directory, update your
>>> subversion checkout (which may update your Enzo tree to reflect  
>>> recent
>>> bug fixes and so on) of both Enzo+yt, and then make sure that all of
>>> the extensions -- of which amr_utils is one! -- are built. Â The 
>>>  last
>>> step is the most important, and you should probably run this every
>>> time you svn up yt. Â I'll make a note of this in the documentat 
>>> ion.
>>>
>>> -Matt
>>>
>>> On Sat, Feb 6, 2010 at 9:28 AM, Agarwal, Shankar <sagarwal at ku.edu>  
>>> wrote:
>>>> Hi,
>>>>
>>>> I just "svn up" my working yt copy (I did not have the  
>>>> volume_rendering earlier). Do I have to "make clean; make" again.
>>>>
>>>> I just tried to run the script...
>>>>
>>>> http://casa.colorado.edu/~skillman/research_and_codes/assets/rot_evolve.txt
>>>>
>>>> on my dataset. But I am getting this error...
>>>>
>>>> Traceback (most recent call last):
>>>> Â File "visual.py", line 6, in <module>
>>>> Â  Â from yt.mods import *
>>>> Â File "/autohome/u118/agarwa23/enzo1.5/src/yt/yt/mods.py", li 
>>>> ne 32, in <module>
>>>> Â  Â import yt.lagos as lagos
>>>> Â File "/autohome/u118/agarwa23/enzo1.5/src/yt/yt/lagos/__init 
>>>> __.py", line 58, in <module>
>>>> Â  Â import yt.amr_utils as amr_utils
>>>> ImportError: No module named amr_utils
>>>> _______________________________________________
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>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
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>>>
>>
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