Hi JC.<div><br></div><div>I remember having a similar build problem now (not the same error) at the last enzo workshop, so here's one last suggestion.</div><div><br></div><div>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!</div>
<div><br></div><div>Best,</div><div>Casey</div><div><br><br><div class="gmail_quote">On Tue, Jan 17, 2012 at 12:38 PM, Jean-Claude Passy <span dir="ltr"><<a href="mailto:jcpassy@gmail.com">jcpassy@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hey Matt,<br>
<br>
not a happy day... :-(<br>
Let me know If you come up with anything. Otherwise, let's try to fix this during the meeting.<br>
<br>
Thanks a lot, and see you soon.<span class="HOEnZb"><font color="#888888"><br>
<br>
JC</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On 17/01/12 14:12, Matthew Turk wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi JC,<br>
<br>
Ah, okay. This sounds more and more like a problem with building<br>
matplotlib. I'm going to recommend a potentially unpopular solution:<br>
wipe your yt-whatever directory, make sure you set CC and CXX, and<br>
build from scratch with a fresh checkout of the install script. My<br>
suspicion is that there is some library -- in this case, likely one of<br>
the matplotlib .so's -- that uses C++, is incorrectly built/linked,<br>
and is causing these funky import errors. This may not fix your<br>
problem, but if it does, that's a happy day. If it does not, we'll<br>
sit down next week and I'll take a look.<br>
<br>
-Matt<br>
<br>
On Tue, Jan 17, 2012 at 2:15 PM, Jean-Claude Passy<<a href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Matt,<br>
<br>
I rebuilt the directory but it did not fix it (I did not have to manually<br>
edit yt/frontends/ramses/setup.py).<br>
I also found out that an 'import pylab' lin the ipython session leads to the<br>
same error.<br>
<br>
Thanks,<br>
<br>
JC<br>
<br>
<br>
On 17/01/12 13:09, Matthew Turk wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi JC,<br>
<br>
This is suspicious. Can you try forcing a rebuild of your yt-hg<br>
directory, and make sure:<br>
<br>
CC=gcc-4.2<br>
CXX=g++-4.2<br>
<br>
Rebuild with:<br>
<br>
python2.7 setup.py build_ext -i -f<br>
<br>
This might fix it. You may also have to manually edit<br>
yt/frontends/ramses/setup.py and ensure that stdc++ is in the<br>
libraries=[] argument for _ramses_reader.pyx.<br>
<br>
-Matt<br>
<br>
On Tue, Jan 17, 2012 at 12:21 PM, Jean-Claude Passy<<a href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a>><br>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi John,<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Does ipython load fine?<br>
</blockquote>
yes, it does.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Can you manually import yt.mods in a python session?<br>
</blockquote>
No, I can't. The error occurs when I try to import it.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Could you check whether a standalone python instance fails with the same<br>
error when you do<br>
<br>
import matplotlib<br>
import h5py<br>
import numpy<br>
</blockquote>
No problem, I can import all these packages.<br>
<br>
Thanks a lot for you help,<br>
<br>
JC<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I have been using the install script with the regular gcc-4.2 as<br>
suggested:<br>
<br>
------------------------------<u></u>------------------------------<u></u>------<br>
[ 9:12:39] Obiwan:$ CC --version<br>
i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot<br>
3)<br>
------------------------------<u></u>------------------------------<u></u>------<br>
<br>
It is so frustrating... yt was working great on my laptop a couple of<br>
months ago and I did not use it until 2 days ago, mainly to check that<br>
I<br>
was ready for the workshop. May be this shows that one should not spend<br>
a single week without using yt! ;-)<br>
<br>
Thanks for your help guys, I appreciate.<br>
JC<br>
<br>
<br>
On 16/01/12 21:01, Casey W. Stark wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I agree, it sounds like a gcc build issue. Which version did you build<br>
against JC?<br>
<br>
It might take me a while to get to it, but I can try to reproduce it<br>
this week.<br>
<br>
Best,<br>
Casey<br>
<br>
<br>
On Mon, Jan 16, 2012 at 4:53 PM, Matthew Turk<<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a><br>
<mailto:<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>><u></u>> wrote:<br>
<br>
Hi JC,<br>
<br>
Unfortunately I'm not really sure -- I no longer have a Mac to<br>
test<br>
against, and this error looks like some deep compilation bug,<br>
likely<br>
with matplotlib. It might be something about your installation<br>
(did<br>
you use the install script? were you using a non-standard GCC?<br>
etc)<br>
but I'm not really sure.<br>
<br>
Anyone else out there, with a Mac, who might be able to give JC a<br>
pointer?<br>
<br>
-Matt<br>
<br>
On Sun, Jan 15, 2012 at 1:56 PM, Jean-Claude Passy<br>
<<a href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a><mailto:<a href="mailto:jcpassy@gmail.com" target="_blank">jcpa<u></u>ssy@gmail.com</a>>> wrote:<br>
> Hey,<br>
><br>
> unfortunately, it does not fix the thing...<br>
> Any other idea?<br>
><br>
> Thanks,<br>
><br>
> JC<br>
><br>
><br>
> On 15/01/12 13:30, Matthew Turk wrote:<br>
>><br>
>> Hi JC,<br>
>><br>
>> My guess is that this is related to using the OSX backend<br>
for<br>
>> Matplotlib. If you can, could you set (in ~/.matplotlibrc)<br>
the<br>
>> variable "backend" to be "Agg" it might fix it.<br>
>><br>
>> -Matt<br>
>><br>
>> On Sun, Jan 15, 2012 at 1:33 PM, Jean-Claude<br>
Passy<<a href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a><<u></u>mailto:<a href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a>>><br>
>> wrote:<br>
>>><br>
>>> Hi all,<br>
>>><br>
>>> I am encountering a weird error when trying to execute<br>
yt-unstable on my<br>
>>> MacBook Pro (10.6.8):<br>
>>><br>
>>><br>
------------------------------<u></u>------------------------------<u></u>----<br>
>>> [13:26:06] Obiwan:$ iyt<br>
>>> terminate called after throwing an instance of<br>
>>> '__gnu_cxx::__concurrence_<u></u>lock_error'<br>
>>> what(): __gnu_cxx::__concurrence_lock_<u></u>error<br>
>>> Abort trap<br>
>>><br>
------------------------------<u></u>------------------------------<u></u>----<br>
>>><br>
>>> I re-installed everything successfully but the error is<br>
still<br>
there.<br>
>>> Any help will be much appreciated!<br>
>>><br>
>>> Thanks a lot,<br>
>>><br>
>>> JC<br>
>>> ______________________________<u></u>_________________<br>
>>> yt-users mailing list<br>
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