[yt-users] mac yt installer issues

Matthew Turk matthewturk at gmail.com
Mon Dec 6 06:55:11 PST 2010


Hi Cameron,

I am unable to replicate your error.  Could you make sure your
LD_LIBRARY_PATH and PYTHONPATH match what was output by the
installation script?  If that doesn't work, I'd suggest you put this
into a script:

import numpy
import matplotlib
from yt.mods import *

and then run this on the command line:

gdb /path/to/yt/installed/python

And just do:

run that_script.py

inside gdb.  This will tell us which module has been incorrectly
linked, which I believe is the actual problem.  We can iterate a bit
back and forth off-list, but for me the installation went off without
a hitch.  My guess is that it's matplotlib, and it's a freetype
linking problem, but I'm not sure yet.

-Matt

On Sun, Dec 5, 2010 at 10:35 PM, Cameron Hummels
<chummels at astro.columbia.edu> wrote:
> At the risk of asking another dumb question, I've encountered another
> bug with the mac install of yt that I wanted to investigate.  The
> installer completed without any further problem, as I mentioned in the
> previous email.  Unfortunately, when I go to actually run yt, I get a
> strange error:
>
> $ python
> Python 2.6.3 (r263:75183, Dec  2 2010, 18:20:57)
> [GCC 4.2.1 (Apple Inc. build 5664)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> from yt.mods import *
> python(29204) malloc: *** error for object 0x101e800e0: pointer being
> freed was not allocated
> *** set a breakpoint in malloc_error_break to debug
> Abort
>
> Ideas?  I guess I could narrow this down by individually loading each of
> the yt modules to find out where the bug is, or at the very least
> putting pdb breakpoints, but I wanted to check first to see if other
> people had encountered this error.  This is with the latest version of
> yt, as I just pulled it from the mercurial repo (unstable).
>
> Cameron
>
> On 12/2/10 6:29 PM, Cameron Hummels wrote:
>> Hi Matt,
>>
>>> At this point, I'd recommend getting the install script from:
>>>
>>> http://hg.enzotools.org/yt/raw-file/yt/doc/install_script.sh
>>>
>>> so that you're on the latest development version.  I believe I've now
>>> fixed the bzlib problem in the development tip version.
>> It looks like you're right.  When I grab the newer version, I don't have
>> the bzlib problem.  Thanks!
>>
>>> As for the second error, some light googling indicates that it may be
>>> a conflict between GCC versions provided by Apple versus those
>>> provided by the FSF.  Do you happen to know if the 'gcc' that comes up
>>> in your path is /usr/bin/gcc, or rather something installed by
>>> MacPorts or maybe from hpc.sf.net ?  It should be the one from Apple,
>>> which I believe is in /usr/bin/gcc.  If you're pulling in
>>> /usr/local/bin/ before /usr/bin, for instance, this could be the
>>> reason for the problem.
>>>
>>> I looked over the Python build options and I don't see one to
>>> explicitly exclude what we're seeing; I've tested the script on my
>>> laptop
>>> right now and it worked, but I also use the Apple GCC.  (I did find an
>>> option that may make static linking a lot easier, however.)  I suspect
>>> that shuffling your path about will fix the issues, but it's possible
>>> there may be another option I'm not seeing right now -- so let me know
>>> if that works or not.
>> You were correct.  My macports installed an alternate version of gcc
>> into the /usr/local/bin, which was first in my path.  After some
>> googling, I was able to lightly modify a file in the CoreFoundation
>> framework that allowed me to make progress (as per this description:
>> http://gcc.gnu.org/bugzilla/show_bug.cgi?id=44981), but then I ran into
>> a few more errors down the road.
>>
>> So I just tried starting over the whole thing with the different version
>> of gcc (the mac version), and everything works fine.  Thanks, Matt!
>>
>> Cameron
>>
>>> -Matt
>>>
>>> On Wed, Dec 1, 2010 at 11:56 PM, Cameron Hummels
>>> <chummels at astro.columbia.edu> wrote:
>>>> Howdy,
>>>>
>>>> I went to grab the latest version of yt and reinstall it on my intel
>>>> snow-leopard mac book pro, and I get a failure part of the way through the
>>>> installer.
>>>>
>>>> $ wget http://hg.enzotools.org/yt/raw-file/stable/doc/install_script.sh
>>>> $ bash install_script.sh
>>>>
>>>> I got an error with BZLIB, so I just unchecked it from the installer and
>>>> started over.  Everything was going to plan, but then I received an error in
>>>> the middle of the Python installation when it tried to compile some
>>>> mactoolboxglue file in yt's python subdir.  Has anyone else encountered this
>>>> problem?  I haven't don't anything too screwy to this box, so I'm wondering
>>>> where things went awry.
>>>>
>>>> Cameron
>>>>
>>>>
>>>> Here are the last few lines from the yt_install.log:
>>>>
>>>> gcc -c -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
>>>> -Wstrict-prototypes  -I. -IInclude -I./Include   -DPy_BUILD_CORE -o
>>>> Python/mactoolboxglue.o Python/mactoolboxglue.c
>>>> In file included from
>>>> /System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:43:0,
>>>>                  from
>>>> /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:20,
>>>>                  from
>>>> /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20,
>>>>                  from
>>>> /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:21,
>>>>                  from
>>>> /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20,
>>>>                  from Include/pymactoolbox.h:10,
>>>>                  from Python/mactoolboxglue.c:27:
>>>> /System/Library/Frameworks/CoreFoundation.framework/Headers/CFBundle.h:147:1:
>>>> error: format string argument not a string type
>>>> make: *** [Python/mactoolboxglue.o] Error 1
>>>>
>>>>
>>>>
>>>>
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