[yt-users] Mecurial compilation error

[Stella Offner]

Hi Matt,

Thanks, that worked. However, even though the install seems successful 
now the script complains it can't find the mecurial libraries:
/n/home05/soffner/yt-x86_64/bin/python2.7: can't open file 
'/n/home05/soffner/yt-x86_64/src/yt-hg//distribute_setup.py': [Errno 2] 
No such file or directory
abort: couldn't find mercurial libraries in 
[/n/home05/soffner/yt-x86_64/python/2.7/site-packages 
/n/home05/soffner/yt-x86_64/bin 
/n/sw/python-2.7/lib/python2.7/site-packages/h5py-1.3.1_beta-py2.7-linux-x86_64.egg 
/n/sw/python-2.7/lib/python2.7/site-packages/lxml-2.3beta1-py2.7-linux-x86_64.egg 
/n/sw/python-2.7/lib/python2.7/site-packages/httplib2-0.6.0-py2.7.egg 
/n/home05/soffner/yt-x86_64/lib/python2.7/site-packages 
/n/sw/python-2.7/lib/python27.zip /n/sw/python-2.7/lib/python2.7 
/n/sw/python-2.7/lib/python2.7/plat-linux2 
/n/sw/python-2.7/lib/python2.7/lib-tk 
/n/sw/python-2.7/lib/python2.7/lib-old 
/n/sw/python-2.7/lib/python2.7/lib-dynload 
/n/sw/python-2.7/lib/python2.7/site-packages]

I don't see them anywhere else in my home directory either...
Thanks,
Stella

Matthew Turk wrote:
> Hi Stella,
>
> On Mon, May 23, 2011 at 11:02 AM, Stella Offner <soffner at cfa.harvard.edu> wrote:
>   
>> Hi,
>>
>> I'm attempting to install a new version of yt on the Harvard Odyssey machine
>> (dual Xeon quad core). The install fails when building mecurial. Does anyone
>> recognize this error?
>> ...
>> running build_ext
>> building 'mercurial.base85' extension
>> creating build/temp.linux-x86_64-2.7
>> creating build/temp.linux-x86_64-2.7/mercurial
>> gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
>> -Wstrict-prototypes -fPIC -I/n/sw/python-2.7/include/python2.7 -c
>> mercurial/base85.c -o build/temp.linux-x86_64-2.7/mercurial/base85.o
>> gcc -pthread -shared -L/n/home05/soffner/yt-x86_64/lib/
>> -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/
>> -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/
>> -L/n/home05/soffner/yt-x86_64/lib64/ -L/n/home05/soffner/yt-x86_64/lib/
>> -L/n/home05/soffner/yt-x86_64/lib64/
>> build/temp.linux-x86_64-2.7/mercurial/base85.o -L. -lpython2.7 -o
>> build/lib.linux-x86_64-2.7/mercurial/base85.so
>> /usr/bin/ld: /n/home05/soffner/yt-x86_64/lib//libpython2.7.a(exceptions.o):
>> relocation R_X86_64_32 against `_Py_NoneStruct' can not be used when making
>> a shared object; recompile with -fPIC
>> /n/home05/soffner/yt-x86_64/lib//libpython2.7.a: could not read symbols: Bad
>> value
>> collect2: ld returned 1 exit status
>> error: command 'gcc' failed with exit status 1
>>
>> Python 2.7 seems to work ok, so I don't know what the deal is with the
>> libpython2.7a error.
>> Thanks,
>> Stella
>>     
>
> Unfortunately I do recognize this error.  The PIC error is related to
> "position independent code".  This shows up when you try to link
> against a static library from within a shared library, which is what's
> going on here.  (Having non-PIC code gains you an extra register,
> which is arguably a Big Deal.)  There are two solutions to it -- one
> is to ensure that all the static libraries, like python, are compiled
> and linked with -fPIC.  The other is to avoid building static
> libraries, which is something we should probably be doing anyway.
>
> To get around this, I'd suggest wiping the current directory structure
> so that you can make sure everything is consistent, and on line 430 of
> the install_script changing this:
>
> ( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
>
> to this:
>
> ( ./configure --enable-shared --prefix=${DEST_DIR}/ 2>&1 ) 1>>
> ${LOG_FILE} || do_exit
>
> If this works for you, I'll make it the default in the install script.
>  I would contest this is how it should be anyway, since any benefits
> to static linking -- like having an all-in-one Python, for CNL or for
> frozen embedded stuff -- are generally outside the realm of the
> install script anyway.
>
> -Matt
>
>   
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>>     
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