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@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.

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@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@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@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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