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

Jean-Claude Passy jcpassy at gmail.com
Thu Jan 26 11:28:40 PST 2012


Hi all,

just wanted to let you know that Matt found a solution (as usual)!
I simply had to unset DYLD_LIBRARY_PATH and activate again.

Cheers,

JC

On 17/01/12 15:05, Jean-Claude Passy wrote:
> Hi Casey,
>
> nice try but unfortunately, it does not change anything...
>
> Cheers,
>
> JC
>
> On 17/01/12 15:40, Casey W. Stark wrote:
>> 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 <mailto: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 <mailto: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 <mailto: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>
>>                                 <mailto: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><mailto: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><mailto: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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