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

Casey W. Stark caseywstark at gmail.com
Tue Jan 17 12:40:03 PST 2012


Hi JC.

I remember having a similar build problem now (not the same error) at the
last enzo workshop, so here's one last suggestion.

For some reason the rebuild step above (the build_ext command) does not
modify those .so files. Rather than wiping your install, I think you can
find *all* of the .so files in your yt-hg directory, delete them, and
rebuild. At least, I remember this working when I had uncommitted work that
I could not afford to scrap. Hope it works for you!

Best,
Casey


On Tue, Jan 17, 2012 at 12:38 PM, Jean-Claude Passy <jcpassy at gmail.com>wrote:

> 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:jcpa**ssy at gmail.com<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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