[yt-users] Bug loading Ramses data

[Sam Geen]

OK, new problem. We've fixed this issue, installed scipy (for pymses), 
run a setup.py install, removed the _ramses_reader.so file in case that 
wasn't being replaced, and run install again, and the new version is 
definitely producing a similar problem:

   File "/home/samgeen/Programming/yttest/yt-x86_64/lib/python2.7/site-packages/matplotlib/delaunay/__init__.py", line 8, in<module>
     from matplotlib._delaunay import delaunay
ImportError:/home/samgeen/Programming/yttest/yt-x86_64/lib/python2.7/site-packages/matplotlib/_delaunay.so: undefined symbol: _ZNSt8ios_base4InitD1Ev

Do you have any advice on getting rid of this one? I can't see a 
setup.py file in the matplotlib folder or its subdirectories.

(CC-ed our compute cluster administrator who is helping me figure out 
various install issues)

On 31/05/2011 17:56, Matthew Turk wrote:
> Hi Sam,
>
> Running the symbol through c++filt gives that it resolves back to
> std::ios_base::Init::~Init().  My guess is that this means we need an
> additional "-lstdc++" in the linking line.  Can you try changing, in:
>
> ~/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/setup.py
>
> the call to add_extension by adding:
>
> libraries=["stdc++"],
>
> so that it looks like this:
>
>      config.add_extension("_ramses_reader",
>          ["yt/frontends/ramses/_ramses_reader.pyx"],
>          language="c++",
>          include_dirs=["yt/frontends/ramses/ramses_headers/"],
>          libraries=["stdc++"],
>          depends=glob.glob("yt/frontends/ramses/ramses_headers/*.hh")
>          )
>
> and then forcing a rebuild with:
>
> cd ~/Programming/yttest/yt-x86_64/src/yt-hg/
> python2.7 setup.py build_ext -i -f
>
> And seeing if that fixes it?
>
> -Matt
>
> On Tue, May 31, 2011 at 9:33 AM, Sam Geen<samgeen at astro.ox.ac.uk>  wrote:
>> Hi,
>>
>> I've recently installed YT and I'm getting an error in _ramses_reader.so
>> when I start up YT; error message below. It's missing symbol
>> _ZNSt8ios_base4InitD1Ev; Googling appears to suggest that it's related to
>> Scipy. Am I missing something in the install? Let me know if you need any
>> more information to unpick this one.
>>
>> Thanks!
>>
>> Sam
>>
>> -------
>> samgeen at service0:~/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses>
>> python
>> Python 2.7.1 (r271:86832, May 31 2011, 13:44:37)
>> [GCC Intel(R) C++ gcc 4.3 mode] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> from yt.mods import *
>> yt : [DEBUG    ] 2011-05-31 15:57:47,986 Set log level to 0
>> WARNING : Can't import tables module...
>> yt : [DEBUG    ] 2011-05-31 15:57:48,476 SIGUSR1 registered for traceback
>> printing
>> yt : [DEBUG    ] 2011-05-31 15:57:48,476 SIGUSR2 registered for IPython
>> Insertion
>> yt : [DEBUG    ] 2011-05-31 15:57:48,582 Registering: StaticOutput as<class
>> 'yt.data_objects.static_output.StaticOutput'>
>> yt : [DEBUG    ] 2011-05-31 15:57:48,593 Registering: EnzoStaticOutput as
>> <class 'yt.frontends.enzo.data_structures.EnzoStaticOutput'>
>> yt : [DEBUG    ] 2011-05-31 15:57:48,594 Registering:
>> EnzoStaticOutputInMemory as<class
>> 'yt.frontends.enzo.data_structures.EnzoStaticOutputInMemory'>
>> yt : [DEBUG    ] 2011-05-31 15:57:48,599 Registering: OrionStaticOutput as
>> <class 'yt.frontends.orion.data_structures.OrionStaticOutput'>
>> yt : [DEBUG    ] 2011-05-31 15:57:48,603 Registering: FLASHStaticOutput as
>> <class 'yt.frontends.flash.data_structures.FLASHStaticOutput'>
>> yt : [DEBUG    ] 2011-05-31 15:57:48,605 Registering: TigerStaticOutput as
>> <class 'yt.frontends.tiger.data_structures.TigerStaticOutput'>
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in<module>
>>   File
>> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/mods.py",
>> line 68, in<module>
>>    from yt.frontends.ramses.api import \
>>   File
>> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/api.py",
>> line 31, in<module>
>>    from .data_structures import \
>>   File
>> "/panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py",
>> line 37, in<module>
>>    import _ramses_reader
>> ImportError:
>> /panfs/panasas/home/samgeen/Programming/yttest/yt-x86_64/src/yt-hg/yt/frontends/ramses/_ramses_reader.so:
>> undefined symbol: _ZNSt8ios_base4InitD1Ev
>> --------
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