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@gmail.comwrote:
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 Passyjcpassy@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 Passyjcpassy@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@gmail.com >> mailto:matthewturk@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@gmail.com<mailto:jcpa**ssy@gmail.comjcpassy@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@gmail.com<**mailto:jcpassy@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 >> >>> ______________________________**_________________ >> >>> yt-users mailing list >> >>> >> yt-users@lists.spacepope.org<**mailto:yt-users@lists.** >> spacepope.org yt-users@lists.spacepope.org> >> >>> >> http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> ______________________________**_________________ >> yt-users mailing list >> yt-users@lists.spacepope.org<**mailto:yt-users@lists.** >> spacepope.org yt-users@lists.spacepope.org> >> http://lists.spacepope.org/**listinfo.cgi/yt-users-** >> spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> >> ______________________________**_________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.orghttp://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > ______________________________**_________________
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