[yt-users] ramses_reader broken on Lens?

gso at physics.ucsd.edu gso at physics.ucsd.edu
Thu Jun 9 13:45:03 PDT 2011


The system admin tracked it down.  He first said he couldn't reproduce my
error that's when I tried to run YT on the login node just to see if
things work without the batch, and it did, so I figured something was
wrong with my submission script.

it turned out I didn't have the line:

#PBS -V

even though I sourced the .Lens_profile (my .bashrc) with the right
modules and PYTHONPATH etc, I needed the PBS option to keep the other
default environment variables.

So I now have a working YT on Lens!  Thanks for all the help.

From
G.S.

> 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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