[yt-users] error launching yt: __gnu_cxx::__concurrence_lock_error
Jean-Claude Passy
jcpassy at gmail.com
Tue Jan 17 13:05:36 PST 2012
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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