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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:<br>
<pre wrap=""> File "<i class="moz-txt-slash"><span class="moz-txt-tag">/</span>home/samgeen/Programming/yttest/yt-x86_64/lib/python2.7/site-packages/matplotlib/delaunay<span class="moz-txt-tag">/</span></i>__init__.py", line 8, in <module>
from matplotlib._delaunay import delaunay
ImportError: <i class="moz-txt-slash"><span class="moz-txt-tag">/</span>home/samgeen/Programming/yttest/yt-x86_64/lib/python2.7/site-packages/matplotlib<span class="moz-txt-tag">/</span></i>_delaunay.so: undefined symbol: _ZNSt8ios_base4InitD1Ev
</pre>
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.<br>
<br>
(CC-ed our compute cluster administrator who is helping me figure
out various install issues)<br>
<br>
On 31/05/2011 17:56, Matthew Turk wrote:
<blockquote
cite="mid:BANLkTi=G6QMWqPEtLtDMBXi5NF1TNYyWQA@mail.gmail.com"
type="cite">
<pre wrap="">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 <a class="moz-txt-link-rfc2396E" href="mailto:samgeen@astro.ox.ac.uk"><samgeen@astro.ox.ac.uk></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">from yt.mods import *
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">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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