[yt-users] ramses_reader broken on Lens?

[Matthew Turk]

Hi G.S.,

When you update, try copying $YT_DEST/src/yt-hg/doc/activate* to
$YT_DEST/bin/ and see if the activate scripts fix it.

-Matt

On Wed, Jun 8, 2011 at 1:01 PM,  <gso at physics.ucsd.edu> wrote:
> Yeah after updating, now matplotlib is complaining.
> I'll see if they can install/find the missing software, I don't think it
> is feasible to rewrite all my scripts just for this one machine.
>
> From
> G.S.
>
>> Actually, it's a different error.  Now you're getting it from the ART
>> import.  I have made the same modification there in 749ce1a696de.
>>
>> The error is still with your environment; it's telling you right in
>> the error message that it's unable to find GLIBCXX.  This is the C++
>> standard library.  I would bet that you will run into more problems
>> down the line -- probably with matplotlib.  However, you should be
>> able to make image plots and serialize data with cPickle to avoid
>> having to use matplotlib.
>>
>> -Matt
>>
>> On Wed, Jun 8, 2011 at 10:25 AM,  <gso at physics.ucsd.edu> wrote:
>>> The modules I have loaded are:
>>> -bash-3.2$ module list
>>> Currently Loaded Modulefiles:
>>>  1) moab                  2) python/2.7            3) PE-gnu/4.4.4
>>>  4) ompi/1.4.2-gnu4.4.4   5) gcc/4.4.4             6) DefApps
>>>
>>> my environment variables are:
>>> export PATH=.:/ccs/home/geoso/LensYT/bin:$PATH
>>> export
>>> PYTHONPATH=/ccs/home/geoso/LensYT/lib:/ccs/home/geoso/LensYT/lib/python
>>> export LD_LIBRARY_PATH=/ccs/home/geoso/LensYT/lib:$LD_LIBRARY_PATH
>>> export MPLCONFIGDIR=/tmp/work/geoso
>>>
>>> and the python in this terminal is pointed to
>>> -bash-3.2$ which python
>>> ~/LensYT/bin/python
>>>
>>> did a yt instinfo -u
>>>
>>> The current version of the code is:
>>>
>>> ---
>>> 716698ff4046 (yt) tip
>>> ---
>>>
>>> but the same error persists.
>>>
>>> From
>>> G.S.
>>>
>>>
>>>> Hi Geoffrey,
>>>>
>>>> If I understand your email correctly, you are loading the GNU
>>>> environment correctly, but it's not entirely clear to me from reading
>>>> it.  I've pushed a fix that will allow ramses_reader to fail silently
>>>> on import.  This is in changeset 716698ff4046.
>>>>
>>>> You may get similar errors with Matplotlib.
>>>>
>>>> Loading PE-pgi will only complicate matters.
>>>>
>>>> -Matt
>>>>
>>>> On Wed, Jun 8, 2011 at 10:01 AM,  <gso at physics.ucsd.edu> wrote:
>>>>> I thought I might have used PE-pgi, so I went and reinstalled YT with
>>>>> the
>>>>> PE-gnu loaded, and installed mpi4py afterwards with the same window
>>>>> specifying --home=/ccs/home/geoso/LensYT when I did the python
>>>>> setup.py
>>>>> install.  And I'm still getting the same error.  I think I recall if I
>>>>> had
>>>>> PE-pgi loaded, mpi4py wouldn't even build.
>>>>>
>>>>> I've even tried loading pgi to run the script and still the same
>>>>> error.
>>>>>
>>>>> From
>>>>> G.S.
>>>>>
>>>>>> Hi Geoffrey,
>>>>>>
>>>>>> This is usually caused by having the wrong programming environment
>>>>>> loaded when you run or build yt.  Did you have GNU loaded when you
>>>>>> built, and do you have it loaded now?
>>>>>>
>>>>>> The reason it shows up with Ramses is that Ramses uses C++.
>>>>>>
>>>>>> -Matt
>>>>>>
>>>>>> On Wed, Jun 8, 2011 at 9:01 AM,  <gso at physics.ucsd.edu> wrote:
>>>>>>> I was trying to test Lens with a fresh install of the devel YT and
>>>>>>> some
>>>>>>> simple projections and I got the following:
>>>>>>>
>>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>>  File "moviesDens.py", line 3, in <module>
>>>>>>>    from yt.mods import *
>>>>>>>  File "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/mods.py", line 71,
>>>>>>> in
>>>>>>> <module>
>>>>>>>    from yt.frontends.ramses.api import \
>>>>>>>  File
>>>>>>> "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/api.py",
>>>>>>> line 31, in <module>
>>>>>>>    from .data_structures import \
>>>>>>>  File
>>>>>>> "/autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/data_structures.py",
>>>>>>> line 37, in <module>
>>>>>>>    import _ramses_reader
>>>>>>> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not
>>>>>>> found
>>>>>>> (required by
>>>>>>> /autofs/na1_home/geoso/LensYT/src/yt-hg/yt/frontends/ramses/_ramses_reader.so)
>>>>>>>
>>>>>>> Is this missing GLIBCXX_3.4.11 YT's problem or should I email the
>>>>>>> NCCS
>>>>>>> sys
>>>>>>> admins?
>>>>>>>
>>>>>>> From
>>>>>>> G.S.
>>>>>>>
>>>>>>> _______________________________________________
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