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@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 -------- _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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