[yt-users] Bug loading Ramses data

[Matthew Turk]

Hi Sam,

This is another interesting one.  Can you check if this works?

import yt.utilities.delaunay

We've been including the delaunay code in yt (since before it was in
matplotlib!) and it's one location that, again, c++ is used.  Can you
check to make sure that the same C++ and C compilers were used for the
yt install?  (i.e., GCC/G++ everywhere)

Thanks,

Matt

On Thu, Jun 2, 2011 at 4:44 AM, Sam Geen <samgeen at astro.ox.ac.uk> wrote:
> 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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