[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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