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.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@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@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:jcpassy@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
>>> _______________________________________________
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>>>
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