[yt-users] error launching yt: __gnu_cxx::__concurrence_lock_error

Jean-Claude Passy jcpassy at gmail.com
Tue Jan 17 11:15:56 PST 2012


Hi Matt,

I rebuilt the directory but it did not fix it (I did not have to 
manually edit yt/frontends/ramses/setup.py).
I also found out that an 'import pylab' lin the ipython session leads to 
the same error.

Thanks,

JC

On 17/01/12 13:09, Matthew Turk wrote:
> Hi JC,
>
> This is suspicious.  Can you try forcing a rebuild of your yt-hg
> directory, and make sure:
>
> CC=gcc-4.2
> CXX=g++-4.2
>
> Rebuild with:
>
> python2.7 setup.py build_ext -i -f
>
> This might fix it.  You may also have to manually edit
> yt/frontends/ramses/setup.py and ensure that stdc++ is in the
> libraries=[] argument for _ramses_reader.pyx.
>
> -Matt
>
> On Tue, Jan 17, 2012 at 12:21 PM, Jean-Claude Passy<jcpassy at gmail.com>  wrote:
>> Hi John,
>>> Does ipython load fine?
>> yes, it does.
>>
>>> Can you manually import yt.mods in a python session?
>> No, I can't. The error occurs when I try to import it.
>>
>>> Could you check whether a standalone python instance fails with the same
>>> error when you do
>>>
>>> import matplotlib
>>> import h5py
>>> import numpy
>> No problem, I can import all these packages.
>>
>> Thanks a lot for you help,
>>
>> JC
>>
>>
>>>> Hi,
>>>>
>>>> I have been using the install script with the regular gcc-4.2 as
>>>> suggested:
>>>>
>>>> ------------------------------------------------------------------
>>>> [ 9:12:39] Obiwan:$ CC --version
>>>> i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>>>> ------------------------------------------------------------------
>>>>
>>>> It is so frustrating... yt was working great on my laptop a couple of
>>>> months ago and I did not use it until 2 days ago, mainly to check that I
>>>> was ready for the workshop. May be this shows that one should not spend
>>>> a single week without using yt! ;-)
>>>>
>>>> Thanks for your help guys, I appreciate.
>>>> JC
>>>>
>>>>
>>>> On 16/01/12 21:01, Casey W. Stark wrote:
>>>>> I agree, it sounds like a gcc build issue. Which version did you build
>>>>> against JC?
>>>>>
>>>>> It might take me a while to get to it, but I can try to reproduce it
>>>>> this week.
>>>>>
>>>>> Best,
>>>>> Casey
>>>>>
>>>>>
>>>>> On Mon, Jan 16, 2012 at 4:53 PM, Matthew Turk<matthewturk at gmail.com
>>>>> <mailto:matthewturk at gmail.com>>    wrote:
>>>>>
>>>>>      Hi JC,
>>>>>
>>>>>      Unfortunately I'm not really sure -- I no longer have a Mac to test
>>>>>      against, and this error looks like some deep compilation bug, likely
>>>>>      with matplotlib. It might be something about your installation (did
>>>>>      you use the install script? were you using a non-standard GCC? etc)
>>>>>      but I'm not really sure.
>>>>>
>>>>>      Anyone else out there, with a Mac, who might be able to give JC a
>>>>>      pointer?
>>>>>
>>>>>      -Matt
>>>>>
>>>>>      On Sun, Jan 15, 2012 at 1:56 PM, Jean-Claude Passy
>>>>>      <jcpassy at gmail.com<mailto:jcpassy at gmail.com>>    wrote:
>>>>>      >    Hey,
>>>>>      >
>>>>>      >    unfortunately, it does not fix the thing...
>>>>>      >    Any other idea?
>>>>>      >
>>>>>      >    Thanks,
>>>>>      >
>>>>>      >    JC
>>>>>      >
>>>>>      >
>>>>>      >    On 15/01/12 13:30, Matthew Turk wrote:
>>>>>      >>
>>>>>      >>    Hi JC,
>>>>>      >>
>>>>>      >>    My guess is that this is related to using the OSX backend for
>>>>>      >>    Matplotlib. If you can, could you set (in ~/.matplotlibrc) the
>>>>>      >>    variable "backend" to be "Agg" it might fix it.
>>>>>      >>
>>>>>      >>    -Matt
>>>>>      >>
>>>>>      >>    On Sun, Jan 15, 2012 at 1:33 PM, Jean-Claude
>>>>>      Passy<jcpassy at gmail.com<mailto:jcpassy at gmail.com>>
>>>>>      >>    wrote:
>>>>>      >>>
>>>>>      >>>    Hi all,
>>>>>      >>>
>>>>>      >>>    I am encountering a weird error when trying to execute
>>>>>      yt-unstable on my
>>>>>      >>>    MacBook Pro (10.6.8):
>>>>>      >>>
>>>>>      >>>
>>>>>   ----------------------------------------------------------------
>>>>>      >>>    [13:26:06] Obiwan:$ iyt
>>>>>      >>>    terminate called after throwing an instance of
>>>>>      >>>    '__gnu_cxx::__concurrence_lock_error'
>>>>>      >>>    what(): __gnu_cxx::__concurrence_lock_error
>>>>>      >>>    Abort trap
>>>>>      >>>
>>>>>   ----------------------------------------------------------------
>>>>>      >>>
>>>>>      >>>    I re-installed everything successfully but the error is still
>>>>>      there.
>>>>>      >>>    Any help will be much appreciated!
>>>>>      >>>
>>>>>      >>>    Thanks a lot,
>>>>>      >>>
>>>>>      >>>    JC
>>>>>      >>>    _______________________________________________
>>>>>      >>>    yt-users mailing list
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>>>>>
>>>>>
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