[yt-users] error launching yt: __gnu_cxx::__concurrence_lock_error
Jean-Claude Passy
jcpassy at gmail.com
Tue Jan 17 12:38:57 PST 2012
Hey Matt,
not a happy day... :-(
Let me know If you come up with anything. Otherwise, let's try to fix
this during the meeting.
Thanks a lot, and see you soon.
JC
On 17/01/12 14:12, Matthew Turk wrote:
> 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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