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

Matthew Turk matthewturk at gmail.com
Tue Jan 17 11:12:57 PST 2012 

Hi JC,

Ah, okay.  This sounds more and more like a problem with building
matplotlib.  I'm going to recommend a potentially unpopular solution:
wipe your yt-whatever directory, make sure you set CC and CXX, and
build from scratch with a fresh checkout of the install script.  My
suspicion is that there is some library -- in this case, likely one of
the matplotlib .so's -- that uses C++, is incorrectly built/linked,
and is causing these funky import errors.  This may not fix your
problem, but if it does, that's a happy day.  If it does not, we'll
sit down next week and I'll take a look.

-Matt

On Tue, Jan 17, 2012 at 2:15 PM, Jean-Claude Passy <jcpassy at gmail.com> wrote:
> 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
>>>>>>     >>>    _______________________________________________
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